United States Court of Appeals for the Federal Circuit 

05-5014 

COMPUTERVISION CORPORATION, 

 

 Plaintiff-Appellant, 

v. 

UNITED STATES, 

Defendant-Appellee. 

John S. Brown, Bingham McCutchen LLP, of Boston, Massachusetts, argued for 

plaintiff-appellant. With him on the brief were George P. Mair, Donald-Bruce Abrams

and Matthew D. Schnall. 

Bruce R. Ellisen, Attorney, Tax Division, United States Department of Justice, of 

Washington, DC, argued for defendant-appellee. With him on the brief were Eileen J. 

O’Connor, Assistant Attorney General; Richard T. Morrison, Deputy Assistant Attorney 

General; and Gilbert S. Rothenberg and Francesca U. Tamami, Attorneys. 

Appealed from: United States Court of Federal Claims 

Judge Marian Blank Horn 
United States Court of Appeals for the Federal Circuit 

05-5014 

COMPUTERVISION CORPORATION, 

 Plaintiff-Appellant, 

v. 

UNITED STATES, 

 Defendant-Appellee. 

 ___________________________ 

 DECIDED: April 20, 2006 

 ___________________________ 

Before NEWMAN, RADER, and DYK, Circuit Judges. 

DYK, Circuit Judge. 

Computervision Corporation (“Computervision”) appeals the decision of the 

United States Court of Federal Claims which held that Computervision is not entitled to 

a refund of deficiency interest assessed and paid with respect to its 1982 tax year. The 

court granted the United States’ motion to dismiss on the ground that the statute of 

limitations barred an interest suspension claim because the plaintiff failed to file a claim 

with the Internal Revenue Service (“IRS”) until more than 10 years after the expiration of 

the two year limitation period of 26 U.S.C. § 6511(a). The court also held that an 

interest netting claim failed to state a claim because the requirements of 26 U.S.C. § 

6621(d) were not met under our decision in Federal National Mortgage Ass’n v. United 

States, 379 F.3d 1303 (Fed. Cir. 2004). We affirm. 
BACKGROUND 

The facts of this case are not in dispute. On September 14, 1983,

Computervision, a manufacturer of computer-aided manufacturing products, overpaid its 

tax liability shown on its 1982 return by $4,750,231, and elected to apply this

overpayment to its 1983 tax year.

1

 On September 17, 1984, Computervision overpaid 

the amount of taxes shown on the 1983 return by $7,329,276, and again elected to 

apply this overpayment to the following year, the 1984 tax year. Finally, on July 2, 

1985, Computervision filed a return for the 1984 tax year showing an overpayment of 

$7,166,031, and requested a refund of the entire amount. The IRS paid the refund,

without interest, on August 2, 1985. 

Following an audit, the IRS issued an “examination report” on January 7, 1986, in 

which it asserted that the taxpayer’s 1982 return had understated its tax liability and 

proposed a deficiency of $6,224,982 for the 1982 tax year. A portion of this deficiency

resulted from the IRS’s determination that a subsidiary of Computervision, 

Computervision International, Inc. (CVI), did not qualify as a domestic international 

sales corporation, or DISC, during the 1983 tax year. See 26 U.S.C. § 992(a)(1)

(1982).2

 Another portion of the deficiency concerned what we refer to as non-DISC 

issues. 

 1 Under 26 U.S.C. § 6402(b), the IRS permits a corporate taxpayer that has 

overpaid its liability in one year to claim a credit for the overpayment against its

estimated taxes for the succeeding year. 26 U.S.C. § 6402(b) (2000). 

2 The DISC provisions allow a domestic production company to establish a 

DISC to handle its export sales and leases. The DISC itself is not subject to tax on its

earnings. 26 U.S.C. § 991 (2000). Instead, a portion of the DISC’s earnings is taxed to

the DISC’s shareholders as a constructive dividend, 26 U.S.C. § 995(b)(1), and the 

remaining income is not taxed to the shareholders until distributed. 26 U.S.C. § 995;

05-5014 2
On April 11, 1986, Computervision submitted a protest regarding the IRS’s 

position with respect to the 1982 tax year to the Boston Appeals Office of the IRS, 

disputing among other issues the determination that CVI was not a DISC. The nonDISC issues in the examination report were resolved by an agreement that the tax 

liability relating to the non-DISC issues was $2,215,952.3

 The IRS proposed a total 

1982 tax deficiency of $7,886,409. Of that amount, $5,670,457 was attributable to the 

DISC issue, and $2,215,952 to non-DISC issues. 

A 1985 net operating loss carryback eliminated all of the proposed 1982 

deficiency (except for a deficiency of $37,776 attributable to investment tax credit 

recapture). However, the carryback did not eliminate Computervision’s liability for

interest which had accrued on the 1982 deficiency. On June 3, 1988, the IRS assessed 

Computervision deficiency interest totaling $4,095,974.42, plus tax in the amount of

$37,776. After corrections, the $4,095,974 interest assessment was revised to 

$4,063,073. Importantly for purposes of this appeal, the $4,063,073 interest

assessment included (1) interest in the amount of $2,808,888 attributable to the stilldisputed DISC qualification issue, and (2) interest in the amount of $1,254,186 

attributable to the resolved non-DISC issues. The IRS computed the deficiency interest 

based on the entire 1982 deficiency amount, from the due date of the 1982 return to the 

due date of the 1985 return (when the NOL carryback offset the deficiency). 

Computervision paid the $37,776 tax deficiency on March 7, 1989. Computervision 

eventually also paid the deficiency interest claimed by the IRS, with the final payment of 

$4,045,011.64 occurring on April 28, 1989. 

 

see Dow Corning Corp. v. United States, 984 F.2d 416, 417 (Fed. Cir. 1993). 

05-5014 3
The statute bars suit for recovery of the deficiency interest unless “a claim for 

refund . . . has been duly filed with the [IRS] . . . .” 26 U.S.C. § 7422(a) (2000). A claim 

is timely filed if filed “within 3 years from the time the return was filed or 2 years from the 

time the tax was paid, whichever . . . expires the later . . . .” 26 U.S.C. § 6511(a). 

Within two years of the final payment, on August 4, 1989, Computervision filed a refund 

claim with the IRS (the “original refund claim”), in which it claimed “that portion of the 

interest relating to the [DISC] disqualification issue” for the 1982 tax year. The refund 

claim specifically requested $2,808,888, the amount of interest assessed by the IRS on 

the DISC tax liability. The refund claim also included a boilerplate provision stating that: 

Computervision claims as a basis for the refund of the interest paid with 

respect to its 1982 taxable year such other grounds as are shown to be 

appropriate by the tax returns, books and records and the Examination 

Report and related Protest of Computervision and [CVI] for their 

respective tax years ended December 31, 1982, and January 31, 1983. 

J.A. at 1228. 

Section 6532 allows the taxpayer to commence suit six months after filing a 

refund claim if the IRS fails to disallow the claim during that time. 26 U.S.C. § 6532(a).

By April 4, 1990, the IRS had not acted on the matter, so Computervision filed a 

complaint in the Court of Federal Claims. The complaint alleged that “Computervision is

aggrieved by the defendant’s failure to refund the interest attributable to the purported 

disqualification of [CVI] as a DISC.” 

Meanwhile, on November 4, 1993, Computervision filed a petition in the United 

States Tax Court disputing deficiencies that were assessed for two different tax years, 

1983 and 1984—primarily on the theory that the IRS had improperly denied DISC 

 3

 Apparently, this amount was later revised by agreement to $2,102,421. 

05-5014 4
treatment for those years. Proceedings in the Court of Federal Claims relating to the 

1982 tax year interest assessment were stayed pending the resolution of the DISC 

issue by the Tax Court, apparently on the theory that the DISC determination for the 

1983 and 1984 tax years would also resolve the issue for the 1982 tax year. On March 

18, 1996, the Tax Court ruled in Computervision’s favor on the DISC issue, holding that 

CVI qualified as a DISC. Computervision Int’l Corp. v. Comm’r, 71 T.C.M. (CCH) 2450

(1996). The Tax Court’s decision on the DISC issue became final on May 25, 1998.4

Following the resolution of the DISC issue by the Tax Court, the Court of Federal 

Claims lifted its stay with respect to the 1982 tax year proceedings on June 22, 1998. 

Computervision and the Department of Justice (“DOJ”) engaged in settlement 

negotiations relating to the 1982 DISC issue. On July 22, 1998, Congress enacted a 

new provision of 26 U.S.C. § 6621, requiring interest netting, that is, requiring the IRS to 

“apply a zero net interest rate to overlapping periods of mutual indebtedness between a 

taxpayer and the IRS.” Fed. Nat. Mortgage Ass. V. United States, 379 F.3d 1303, 1306 

(2004) (describing 26 U.S.C. § 6621(d)). In May 2, 2000, letters to both DOJ and the 

IRS, Computervision claimed the right to a refund of non-DISC interest based on the 

theory of interest netting under 6621(d). Computervision did not in these letters assert a 

claim for interest suspension. The IRS replied on August 17, 2000, treating the claim as

including an interest suspension claim for 1982. Specifically, the IRS’s August 17 letter 

stated “Revenue ruling 99-40 (Sequa) [interest suspension] is applied regarding the 

credit elect [from the 1982 tax year] to 1983. No claim is necessary.” J.A. at 1405. The 

 4 The Tax Court proceeding remains pending with respect to certain 

computational issues.

05-5014 5
DOJ sent a letter on October 25, 2000, stating that the DOJ was “not in agreement [with 

the IRS computations suggesting] that an additional refund or overpayment can be 

allowed in the instant litigation – over and above that negotiated on the basis of the 

issues in suit – based upon Revenue Ruling 99-40 absent the filing of a timely claim for 

refund raising the issue.” J.A. at 1428 (emphasis in original). In a March 14, 2002, 

letter, the DOJ reiterated its position and stated that “we do not believe that a timely

claim for refund has been filed on [the interest suspension] issue.” J.A. at 1430. 

Computervision filed a formal amendment with the IRS on April 4, 2002, in which it 

claimed non-DISC interest under the interest suspension theory. 

On July 9, 2003, Computervision filed an amended complaint in the Court of 

Federal Claims, claiming $820,946.13 in deficiency interest relating to non-DISC issues 

on theories of interest suspension and interest netting. 

The government contended that the interest suspension claim was barred by the 

statute of limitations. Unlike the DISC interest claim, which involved a challenge to the 

underlying tax liability, the claim for interest suspension did not involve any challenge to 

the underlying deficiencies asserted with respect to the non-DISC issues. Rather, the 

taxpayer contended that, even though the underlying tax liability had been properly

determined with respect to non-DISC issues, interest was not owed. The taxpayer

relied on the principle of interest suspension, which derives from 26 U.S.C. § 6601(a), 

and was formally set out in Revenue Ruling 99-40, published on October 4, 1999, more 

than three years earlier. 1999-2 C.B. 441. Section 6601(a) requires the payment of

interest by the taxpayer with respect to “any amount of tax [that] . . . is not paid on or

before the last date prescribed for payment,” and provides that “interest on such amount 

05-5014 6
. . . shall be paid for the period from such last date to the date paid.” Revenue Ruling 

99-40 addressed “the manner in which interest on a subsequently determined 

deficiency is computed under § 6601(a) when the taxpayer makes an election to apply 

an overpayment to the succeeding year’s estimated taxes.” Id.

Under Revenue Ruling 99-40, interest suspension applies when (a) a taxpayer

elects to credit an overpayment reported on the return for year one [here 1982] to year 

two [here 1983]; (b) a deficiency is subsequently determined for year one [1982]; and 

(c) the credit elect to year two is not “needed” to satisfy the required payments of 

estimated tax for year two [1983]. Rev. Rul. 99-40. Under these circumstances, 

interest is suspended relating to the deficiency for year one [1982]. Here, in other

words, the taxpayer asserted that deficiency interest was not owed for 1982 because 

the tax for that year had been overpaid, and that the credit-elect transferring that 

payment to the 1983 tax year should be ignored for purposes of computing interest. 

Similarly, taxpayer’s credit elect from 1983 to 1984 was not needed to pay its 1984 

liability, because the 1984 taxes had also been overpaid.5

 

As part of the 2003 amended complaint, the taxpayer asserted an alternative 

theory for recovery of the non-DISC interest based on a theory of interest netting. 

“Interest netting” is set forth in 26 U.S.C. § 6621(d), which provides that the IRS applies

a net interest rate of zero to overlapping underpayments and overpayments of tax. With 

respect to interest netting there is a different limitations issue (described below), but 

there is no issue as to whether the claim itself was timely filed with the IRS because the 

 5 The interest suspension theory is described in our decision in Marsh & 

McLennan Cos., Inc. v. United States, 302 F.3d 1369, 1378 (Fed. Cir. 2002). 

05-5014 7
statute provides for retroactive relief if the statutory conditions are satisfied. See 26 

U.S.C. § 6621(d), Pub. L. No. 105-206, § 3301(c)(2), 112 Stat. 741 (1998), as 

amended. The parties agree that interest netting provides identical relief as interest

suspension. 

On September 9, 2004, the Court of Federal Claims rendered a final decision.

Computervision Corp. v. United States, 62 Fed. Cl. 299 (2004). By agreement of the 

parties, the Court of Federal Claims awarded judgment in favor of the taxpayer in the 

amount of $2,997,761.42, representing the deficiency interest paid with respect to the 

DISC deficiency.6

 Id. at 332. However, the Court of Federal Claims granted the 

government’s motion to dismiss the taxpayer’s claim for a refund of deficiency interest 

on the non-DISC deficiencies. It held that the interest suspension claim was barred by 

the statute of limitations because a claim was not filed with the IRS within two years of 

the date of payment as required by 26 U.S.C. § 6511(a). Id. at 328-29. It also held that

Computervision failed to state a claim for interest-netting under section 6621(d). Id. at 

332. Section 6621(d) only applies to overlapping periods when underpayment interest

is “payable” and overpayment interest is “allowable.” The court held that interest is not 

“allowable” on an overpayment credited to a succeeding year’s estimated tax, nor on an 

overpayment refunded within 45 days. Computervision’s 1982 and 1983 overpayments

were credited to succeeding years, and its 1984 overpayment was refunded within 45 

days, so it failed to meet the requirements of section 6621(d). See id. at 331-32. 

The taxpayer timely appealed, and we have jurisdiction pursuant to 26 U.S.C. § 

 6 There is a slight discrepancy between the award of $2,997,761.42 and 

Computervision’s original claim of $2,808,888. 

05-5014 8
1295(a)(3). 

DISCUSSION 

I 

We first address the statute of limitations issue with respect to Computervision’s

interest suspension claim. 

Statutes of limitations play an important role in tax administration, benefiting both 

the government and taxpayers. The government’s authority to assess taxes is limited 

by 26 U.S.C. § 6501, under which taxes must be assessed within three years of the 

filing of the return. 26 U.S.C. § 6501 (2000). Similarly, the taxpayer must file its refund 

claim with the IRS “within 3 years from the time the return was filed or 2 years from the 

time the tax was paid, whichever . . . expires the later . . . .” 26 U.S.C. § 6511(a).7

 Here

the taxpayer’s original claim for refund was filed with the IRS within the limitations 

period because it was filed on August 4, 1989, within two years of the date of the last 

payment, April 28, 1989. However, that claim did not specifically include the interest 

suspension claim with respect to the non-DISC issues. A formal claim with the IRS was

not filed until April 4, 2002, more than 10 years after the limitations period had expired. 

Nonetheless, the taxpayer claims that for a variety of reasons the claim was timely. 

Understanding the taxpayer’s contentions requires a description of the overall 

regulatory scheme. Section 7422(a) of the Internal Revenue Code bars a taxpayer from 

filing a suit for refund “until a claim for refund or credit has been duly filed with the

 7 The taxpayer may file suit for refund after “the expiration of 6 months from 

the date of filing the claim . . . unless the Secretary renders a decision thereon within

that time,” and must file the suit within “2 years from the date of mailing . . . to the

taxpayer of a notice of the disallowance of the part of the claim to which the suit or

proceeding relates.” 26 U.S.C. § 6532(a)(1). 

05-5014 9
Secretary, according to the provisions of law in that regard, and the regulations of the 

Secretary established in pursuance thereof.” 26 U.S.C. § 7422(a) (2000). The 

Secretary by regulation requires that claims for refund “set forth in detail each ground

upon which a credit or refund is claimed and facts sufficient to apprise the 

Commissioner of the exact basis thereof.” 26 C.F.R § 301.6402-2(b)(1) (2005) 

(emphasis added). Earlier regulations contained similar provisions. See, e.g., United 

States v. Kales, 314 U.S. 186, 193 (1941) (citing Article 1306 of Treasury Regulation 

65, promulgated under the 1924 Revenue Act); U.S. Pipe & Foundry, Co. v. United 

States, 155 F. Supp. 231, 232 (Ct. Cl. 1957) (citing Regs. 111, sec. 29.322-3). 

The requirement for filing a proper refund claim “is designed both to prevent 

surprise and to give adequate notice to the Service of the nature of the claim and the 

specific facts upon which it is predicated, thereby permitting an administrative 

investigation and determination.” Alexander Proudfoot Co. v. United States, 454 F.2d 

1379, 1383 (Ct. Cl. 1972) (quoting Union Pac. R.R. v. United States, 389 F.2d 437, 442 

(Ct. Cl. 1968), cert denied, 395 U.S. 944 (1969)). This requirement for claim specificity

applies equally to claims for deficiency interest which are separate from claims for the 

underlying tax liability. John B. Lamert & Assocs. Inc. v. United States, 212 Ct. Cl. 71, 

1986 WL 22198, at *10 (1976). 

The Supreme Court has held that in some circumstances a taxpayer’s claim is

not barred by the statute of limitations even though the taxpayer did not timely file the 

formal, detailed claim required by the regulations. See, e.g., Kales, 314 U.S. at 196-97; 

United States v. Andrews, 302 U.S. 517, 524 (1938); United States v. Memphis Cotton 

Oil Co., 288 U.S. 62, 70-71 (1933); Tucker v. Alexander, 275 U.S. 228, 231 (1927). 

05-5014 10
Unfortunately in implementing the Supreme Court’s decisions the language used to 

describe these exceptions has not always been uniform in courts outside of this circuit. 

In this circuit this aggregation of rules has come to be known as the substantial 

variance doctrine. See Lockheed Martin Corp. v. United States, 210 F.3d 1366, 1371 

(Fed. Cir. 2000); see also Western Co. of N. Am. v. United States, 323 F.3d 1024, 1034 

(Fed. Cir. 2003); Union Pac. R.R., 389 F.2d at 442-47; Armstrong Rubber Co. v. United 

States, 207 Ct. Cl. 1023, 1975 WL 3232, at *1 (1975). The doctrine permits 

consideration of a claim for refund despite failure to timely file detailed formal claims 

with the IRS when a substantial variance from the requirements of the regulation is not

involved.8

 But this doctrine applies only in four limited situations. Each of these has

itself come to be identified as a separate doctrine. 

A 

First, formal compliance with the statute and regulations is excused when the 

informal claim doctrine is applicable. Under the informal claim doctrine, a timely claim 

with purely formal defects is permissible if it fairly apprises the IRS of the basis for the 

claim within the limitations period. 

The informal claim doctrine is best described in the Supreme Court’s decision in

Kales, 314 U.S. 186. There within the limitations period the taxpayer submitted an 

informal letter claiming a refund of tax. The letter did not comply with the IRS’s

regulations because it was not filed on the correct form. The taxpayer later filed an 

 8

 In many cases, the issue is whether there is a substantial variance from a 

timely filed claim. See Lockheed, 210 F.3d 1366 at 1371 (Fed.Cir.2000) (holding that 

taxpayer may not “present[ ] claims in a tax refund suit that ‘substantially vary’ the legal 

theories and factual bases set forth in the tax refund claim presented to the IRS”). 

05-5014 11
untimely amendment that complied with the regulations. The Supreme Court held that 

“a [timely] notice fairly advising the Commissioner of the nature of the taxpayer’s claim .

. . will nevertheless be treated as a[n effective] claim, where formal defects . . . have

been remedied by amendment filed after the lapse of the statutory period.” Id. at 194. 

The informal claim doctrine is well recognized in other circuits.

9

 We and our

predecessor court, the Court of Claims, have specifically applied the doctrine. See, 

e.g., Arch Eng. Co., Inc. v. United States, 783 F.2d 190, 192 (Fed. Cir. 1986); Barenfeld 

v. United States, 442 F.2d 371, 374 (Ct. Cl. 1971); Stuart v. United States, 130 F. Supp.

386, 388-90 (Ct. Cl. 1955); Am. Radiator & Standard Sanitary Corp. v. United States, 

318 F.2d 915, 920-22 (Ct. Cl. 1963). 

In American Radiator the Court of Claims held that “[i]nformal refund claims have 

long been held valid” when they “have a written component . . . [and] adequately 

apprise the Internal Revenue Service that a refund is sought and for certain years.” 318 

F.2d at 920 (citing Kales, 314 U.S. 186). The Court of Claims found that the taxpayer 

 9

 See Kaffenberger v. United States, 314 F.3d 944, 954-957 (8th Cir. 2003) 

(upholding jury verdict permitting untimely amendment to informal claim, where informal 

claim had been filed on “Automatic Extension Request” Form 4868, rather than Form

1040, and the IRS was on notice of claim because the “information held by the IRS 

described the refund sought with sufficient particularity to allow the IRS to investigate 

the claim”); PALA, Inc. v. United States, 234 F.3d 873, 877-79 (5th Cir. 2000) (holding 

that “an informal claim is sufficient if it is filed within the statutory period, puts the IRS on 

notice that the taxpayer believes an erroneous tax has been assessed, and describes

the tax and year with sufficient particularity to allow the IRS to undertake an 

investigation”) (citing Kales, 314 U.S. at 194); BCS Fin. Corp. v. United States, 118 F.3d 

522, 524-25 (7th Cir. 1997) (citing Kales, 314 U.S. at 194); United States v. Commercial 

Nat’l Bank of Peoria, 874 F.2d 1165, 1170-76 (7th Cir. 1989) (permitting untimely 

amendment where taxpayers’ attorney wrote a letter to IRS within limitations period, 

contesting the IRS’s calculations); see also generally Martin v. United States, 833 F.2d 

655, 660, 662-63 (7th Cir. 1987); Michael I. Saltzman, IRS Practice and Procedure

¶ 11.08[2] (2d student ed. 1991) (“IRS Prac. & Proc.”). 

05-5014 12
filed an informal claim by writing “various notations and figures” on its timely filed 

income tax return. Id.; see also Newton v. United States, 163 F. Supp. 614, 619-20 

(Ct. Cl. 1958) (finding informal refund claim based on written protests prior to payment); 

Night Hawk Leasing Co. v. United States, 18 F. Supp. 938, 941-42 (Ct. Cl. 1937)

(finding informal refund claim based on objection on the back of a check paying the tax). 

In Western Co. of North America v. United States, 323 F.3d 1024 (Fed. Cir. 

2003), we recognized that the doctrine applies in circumstances in which the taxpayer’s

action involved a request for information. Western Co., 323 F.3d 1035. The IRS 

mistakenly assessed the taxpayer a “failure-to-file” (“FTF”) penalty. Id.; see also

Western Co. of N. Am. v. United States, 52 Fed. Cl. 51, 54 (2002). The taxpayer, 

unaware of what had caused this penalty, repeatedly requested information about the 

basis for the penalty but did not file a formal claim for a refund. The IRS documented 

this request in writing. 323 F.3d at 1035. We held that the substantial variance doctrine 

did not bar the taxpayer’s refund claim because, during the limitations period, Western 

had “repeated[ly] request[ed] . . . information that would have allowed filing of an 

informed claim,” and thereby “put the IRS on notice of its challenges to [the] false 

assessment.” Id. at 1034-35. 

The informal claim doctrine is of no assistance to the taxpayer here.

Computervision’s original complaint was formal, and contained no specific suggestion 

that non-DISC interest was in dispute. The complaint simply alleged that 

“Computervision is aggrieved by the defendant’s failure to refund the interest 

attributable to the purported disqualification of [CVI] as a DISC.” There was no further 

communication from Computervision to the IRS during the limitations period suggesting 

05-5014 13
that Computervision was asserting a claim for non-DISC interest. As the Court of 

Federal Claims found, “the original claim could not reasonably provide notice to the IRS 

of [the interest suspension claims].” Computervision, 62 Fed. Cl. at 324. Thus, 

Computervision’s refund claim was not a valid informal claim. 

B 

A second exception exists known as the waiver doctrine. If the taxpayer files a 

timely formal claim but fails to include the specific claim for relief, the claim may

nonetheless be considered timely if the IRS considers that specific claim within the 

limitations period. The IRS’s consideration of the specific claim is held to be a waiver of 

the requirement of the regulation that the refund claim “set forth in detail each ground 

upon which a credit or refund is claimed and facts sufficient to apprise the 

Commissioner of the exact basis thereof.” 26 C.F.R. § 301.6402-2(b)(1). 

The Supreme Court recognized the waiver doctrine in Memphis Cotton, 288 U.S. 

62, and Angelus Milling Co. v. Commissioner, 325 U.S. 293 (1945). In Memphis Cotton, 

the Supreme Court found a waiver where (during investigation of the taxpayer’s original

claim and within the limitations period) the Commissioner discovered that the taxpayer

was entitled to a refund on a specific ground, and notified the taxpayer that a refund 

would be made. 288 U.S. at 65, 73. After the limitations period expired, the 

Commissioner reversed its position and refused to grant the refund. The taxpayer then 

filed an amendment asserting its right to a refund. Id. at 65-66. The Court held that the 

amendment was timely because “[l]ong before the amendment the Commissioner had 

ascertained the facts and had even notified the taxpayer of the justice of its claims and 

of the ruling of the Bureau that adjustments would be made accordingly.” Id. at 73. 

05-5014 14
In Angelus Milling, the Court held that the claim was untimely but stated that a 

waiver might be found where “[t]he evidence [is] clear that the Commissioner 

understood the specific claim that was made even though there was a departure from 

form in its submission,” and “[t]he showing [is] unmistakable that the Commissioner has 

in fact seen fit to dispense with [the] formal requirements and to examine the merits of 

the claim.” 325 U.S. at 297; see, e.g., United States v. Garbutt Oil, 302 U.S. 528, 533 

(1938) (“[W]hile the Commissioner might have enforced the regulation and rejected a 

claim for failure to comply with it in omitting to state with particularity the grounds on 

which the claim was based, he was not bound to do so, but might waive the requirement 

of the regulation and consider a general claim on its merits.”). 

Various other courts and authorities have also recognized the waiver doctrine.10 

Our predecessor court also recognized the doctrine. In Consolidated Coppermines

Corp v. United States, 296 F.2d 743, 744 (Ct. Cl. 1961), the Court of Claims held that a 

claim could be filed outside the limitations period if it raised a ground that the IRS had 

discovered, within the limitations period, during investigation of the original claim. The 

court found that “the amendment [filed outside the limitations period] merely made more 

definite the matters already within the knowledge of the Commissioner, which in the

course of his investigation he actually did ascertain.” 296 F.2d at 744 (Ct. Cl. 1961)

(internal quotations and citations omitted); see U.S. Pipe & Foundry, 155 F.Supp. 231, 

232-34 (Ct. Cl. 1957) (“[W]here the Commissioner determines and applies newly

 10 See, e.g., BCS Fin., 118 F.3d at 525-26; Herrington v. United States, 416 

F.2d 1029, 1032 (10th Cir. 1969); IRS Prac. & Proc. ¶ 11.09[5]; Gerald A. Kafka & Rita 

A. Cavanagh, Litigation of Federal Civil Tax Controversies ¶ 16.02[1] (2d ed. 1997 & 

supp. 2005). 

05-5014 15
discovered or different grounds in computing the [taxpayer’s liability] . . . [he] is 

precluded from thereafter denying the refund because the claim was incompatible with 

his regulations . . . .”); Nat’l Forge & Ordnance Co. v. United States, 151 F. Supp 937,

941 (Ct. Cl. 1957) (allowing taxpayer to assert a claim in court where “the claim for 

refund was sufficient to cause the Commissioner to consider the matters which are the 

basis of the present suit”); see also Union Pac. R.R., 389 F.2d at 442 (recognizing that

“an item raised in litigation but not specifically adverted to in the [original] claim might be 

permitted if it is found that . . . the Commissioner considered that unspecified ground in 

reaching his decision on the items for which a refund was requested”). 

The central purpose of the waiver doctrine is “to prevent IRS agents from lulling 

taxpayers into missing the [limitations] deadline . . . .” BCS Fin., 118 F.3d at 526; PALA, 

234 F.3d at 880 (quoting BCS Fin., 118 F.3d at 526). Where the taxpayer learns, within 

the limitations period, that the IRS has addressed the merits of a particular ground, and 

thus fails to file a timely formal claim raising that ground, the taxpayer’s claim is not 

barred. 

However, we agree with the Court of Federal Claims that the IRS cannot waive 

the requirements of its regulations by conduct outside of the limitations period. See

Computervision, 62 Fed. Cl. at 327. In Garbutt Oil, the Commissioner considered the 

merits of a claim for a tax refund after the limitations period had expired. 302 U.S. at 

533. The argument was that the Commissioner had waived the requirements of the 

regulation. The Court held that the claim was not timely, reasoning that “no officer of 

the government has power to waive the statute of limitations . . .” Id. at 534. This

conclusion follows from the statute itself. Even the erroneous allowance of a refund that 

05-5014 16
is barred by the statute of limitations cannot prevent the government from recovering 

that allowance. Section 7405 allows the government to bring suit to recover an 

“erroneous” refund. 26 U.S.C. § 7405(a) & (b). Section 6514 provides that a refund is

“erroneous” if it is made after the expiration of the limitations period and no timely claim 

was filed. 26 U.S.C. § 6514(a)(1). 

Our predecessor court has similarly held that a waiver may not occur after the 

limitations period expires. In Sicanoff Vegetable Oil Corp. v. United States, 181 F.

Supp. 265 (Ct. Cl. 1960), the Court of Claims refused to find a waiver where the 

taxpayer filed timely claim asserting one ground, the limitations period expired, and the 

Commissioner then by mistake considered a different second ground. The taxpayer

filed an untimely amendment asserting the second ground. Id. at 268. The court held 

that the Commissioner “was not permitted by law to pay such a claim, and his 

consideration of it could not enlarge his legal authority.” Id. at 268-69; see also Melchior 

v. United States, 145 F. Supp. 193, 194 (Ct. Cl. 1956). 

The taxpayer relies on a few Excess Profits Tax cases decided in other

jurisdictions for the proposition that the requirements of what is now 26 C.F.R § 

301.6402-2(b)(1) may be waived after the statute of limitations has expired. See Dale

Distrib. Co. v. Comm’r, 269 F.2d 444 (2d Cir. 1959); Eisenstadt Mfg. Co. v. Comm’r, 28

T.C. 221 (1957); Martin Weiner Corp. v. Comm’r, 26 T.C. 128 (1956).11 Many of those 

 11 The taxpayer also relies on Schenley Indus., Inc. v. Comm’r, 42 T.C. 129 

(1964). There the Tax Court held that the IRS “waived” the specificity requirement by

failing to timely raise the variance defense during litigation. Id. at 170; see also Tucker 

v. Alexander, 275 U.S. 228, 230-31 (1927). The issue in the present case is not

whether the government can waive the variance defense through inaction during 

litigation, but rather whether it can waive the defense through administrative action. 

05-5014 17
cases involved special regulations under the Excess Profits provisions that imposed 

unusually detailed claim requirements. See Eisenstadt, 28 T.C. at 231-32; Dale, 269 

F.2d at 445. Those decisions are not binding on this court, and are inconsistent with

Garbutt Oil and Sicanoff if they are viewed as allowing a waiver after the limitations 

period. Moreover, as other circuits have recognized,12 expanding the scope of the 

waiver doctrine as the taxpayer urges would appear to be inconsistent with more recent

Supreme Court authority holding that actions of regulatory authorities cannot either

extend the statute of limitations under section 6511 by equitable tolling or create an 

estoppel against the government. See Brockamp, 519 U.S. 347, 352 (holding that 

equitable tolling does not apply to toll section 6511); Office of Pers. Mgmt. v. Richmond, 

496 U.S. 414, 434 (1990) (holding that conduct of a government agent could not estop 

the government from denying benefits not otherwise permitted by law). The taxpayer 

has not called our attention to any post-Brockamp or Richmond decisions in other

jurisdictions that have applied the waiver doctrine to actions by the IRS taking place 

after the running of the limitations period.13

Here there is no contention that the IRS considered the taxpayer’s claim for nonDISC interest within the limitations period. Rather Computervision contends that the 

IRS waived the specificity requirement nine years after the limitations period expired in 

 12 See BCS Fin., 118 F.3d at 525 (noting that the exceptions are in tension 

with United States v. Brockamp, 519 U.S. 347 (1997), and other Supreme Court 

authority); PALA, 234 F.3d at 880 n.37 (“We share the Seventh Circuit’s concern that 

the Supreme Court’s decision in [Brockamp] calls into question the continuing viability of

the waiver/estoppel strand of the informal claim doctrine.”). 

13 But cf. Kaffenberger, 314 F.3d 944, 953 (8th Cir. 2003) (holding that

explicit waiver authorized under § 6501 allows the IRS and the taxpayer to agree to 

extend the assessment period after statute of limitations expires). 

05-5014 18
an August 17, 2000, letter from the IRS to Computervision that included a set of interest 

computations applying interest suspension to the non-DISC interest. The letter also 

stated that “Revenue ruling 99-40 (Sequa) [interest suspension] is applied regarding the 

credit elect to 1983. No claim is necessary.” J.A. at 1405. Computervision cannot

benefit from the waiver doctrine because the IRS consideration occurred long after the 

expiration of the limitations period. 

C 

A third exception, which we refer to as the general claim doctrine, exists where 

(1) the taxpayer has filed a formal general claim within the limitations period; and (2) an 

amendment is filed outside the limitations period that makes the general claim more 

specific. The Supreme Court described this exception in United States v. Andrews, 302 

U.S. 517, 524 (1938): 

Where a claim which the Commissioner could have rejected as too 

general, and as omitting to specify the matters needing investigation, has 

not misled him but has been the basis of an investigation which disclosed 

facts necessary to his action in making a refund, an amendment which 

merely makes more definite the matters already within his knowledge, or

which, in the course of his investigation, he would naturally have 

ascertained, is permissible. 

The Supreme Court thus recognized that an amendment making a general claim more 

specific may be permissible even when filed outside the limitations period. 

The Supreme Court applied the general claim doctrine in United States v. 

Factors & Fin. Co., 288 U.S. 89 (1933). There the IRS performed an audit of the 

taxpayer, but the audit was incomplete when the statute of limitations expired. In order 

to preserve any claims resulting from the audit, the taxpayer filed a general claim before 

the limitations period expired requesting a refund of all the taxes it had paid. The claim

05-5014 19
did not set forth any specific ground, and explained that its purpose was “to permit the 

Commissioner to refund to deponent any excess paid over taxes actually found to be

due.” Id. at 91. The Court held that the taxpayer’s subsequent amendment was not 

barred by the statute of limitations. Id. at 96. “[A] general claim for refund, not 

specifying grounds, is subject to amendment until final rejection irrespective of a 

limitation running in the interval.” Id. at 93 (citing Memphis Cotton Oil, 288 U.S. 62). 

Similarly, in Memphis Cotton the Court held that an amendment to a general claim, filed 

outside the limitations period, was timely where the original claim merely stated the 

amount of the tax paid, the correct tax and the amount of overpayment, but did not

specify the facts or reasons justifying a refund. 288 U.S. at 64-65, 71. 

Our predecessor court recognized the general claim doctrine in at least one 

case, Cochran v. United States, 62 F. Supp. 872, 872 (Ct. Cl. 1945), where the court 

permitted an untimely amendment to a general claim that requested refunds relating to 

“losses not claimed.” The court held that the amendment “perfected and made specific” 

the original general ground. Id. at 875. 

However, the general claim doctrine only applies when the original claim is

general rather than specific. In United States v. Henry Prentiss & Co., 288 U.S. 73 

(1933), the Supreme Court held that where the original timely claim asserted a specific 

ground, it could not be amended out of time to claim a new basis for relief unrelated to 

the original claim. Id. at 83. Likewise in Andrews the Court found that an amendment

to a claim raising a specific ground was untimely because “[t]he very specification of the 

items of complaint would tend to confine the investigation to those items and there is no 

evidence that the examination was more extended.” 302 U.S. at 525. 

05-5014 20
Here Computervision’s original claim was not general but specific. It contained a 

specific request for DISC-related interest which claimed “the portion of the interest paid 

that is attributable to the [DISC disqualification issue].”14 J.A. at 1225. 

To be sure the original 1989 claim included a secondary, general claim. The 

general claim was a boilerplate provision stating: 

Computervision claims as a basis for the refund of the interest paid with 

respect to its 1982 taxable year such other grounds as are shown to be 

appropriate by the tax returns, books and records and the Examination 

Report and related Protest of Computervision and [CVI] for their 

respective tax years ended December 31, 1982, and January 31, 1983. 

J.A. at 1228. In Andrews the Supreme Court rejected the argument that the general 

claim doctrine was applicable under such circumstances. As here, the taxpayer’s claim

in Andrews “not only called for redress of a specified grievance but demanded general 

relief as well.” 302 U.S. at 525. The Court held that the taxpayer’s amendment was 

barred by the statute of limitations, reasoning that “[t]he very specification of the items of 

complaint would tend to confine the investigation to those items and there is no

evidence that the examination was more extended.” Id. at 526. Thus Computervision’s

untimely claim for non-DISC interest does not meet the requirements of the general 

claim doctrine.15

D 

Where the general claim doctrine is inapplicable because the original claim was

 14 Computervision’s original claim also included an “alternative” claim 

regarding the computation of the so called “DISC Commission” paid by Computervision 

to CVI. 

15 In any event, as discussed immediately below, the amendment had to be 

filed while the IRS still had jurisdiction over the claim, and the IRS no longer had 

jurisdiction once the taxpayer filed the refund suit. 

05-5014 21
not general but specific, a related doctrine, the germaneness doctrine, may allow relief. 

This fourth exception only applies where the taxpayer (1) files a formal claim within the 

limitations period making a specific claim; and (2) after the limitations period but, while 

the IRS still has jurisdiction over the claim, files a formal amendment raising a new legal 

theory--not specifically raised in the original claim--that is “germane” to the original 

claim, that is, it depends upon facts that the IRS examined or should have examined 

within the statutory period while determining the merits of the original claim. Unlike the 

waiver doctrine, the inquiry here is not whether the particular legal theory for recovery 

has been considered by the IRS during the limitations period but whether the underlying 

facts supporting that legal theory were discovered or should have been discovered by 

the IRS in considering the original claim during the limitations period. 

The Supreme Court recognized this exception in Bemis Brothers Bag Co. v. 

United States 289 U.S. 28 (1933). In Bemis, the taxpayer filed a timely claim for a 

refund with the Commissioner, arguing that the Commissioner should allow a so-called 

“special assessment” for determining “invested capital” for excess profits tax purposes 

because invested capital could not be calculated with precision. Id. at 31. To support 

this claim, the taxpayer urged that the precise values of certain items could not be 

ascertained. The Commissioner denied the claim. After the limitations period expired 

but before the refund suit was filed, the taxpayer filed an amendment specifically urging 

that the items should be included in invested capital because they could be calculated, 

and that the tax should be recalculated on that basis. Id. at 31-32. Thus, the taxpayer’s

amendment did not require inquiry into a new set of facts, but simply adapted the form 

of relief to the facts which would have to be examined during investigation of the original 

05-5014 22
claim. The Court held that “the claim as amended does not differ in matter of substance 

from the claim as first presented,” because “[i]f the [Commissioner] found that there had 

been omissions, but that he was able to his own satisfaction to identify and appraise

them, he would learn in the process that there had been an undervaluation of invested 

capital, and that the assessment of the tax was correspondingly erroneous.” Id. at 35. 

This doctrine also was described in the Supreme Court’s decision in Andrews. 

There, in addition to holding that the general claim was inadequate because it was 

accompanied by a specific claim, the court held the specific claim was inadequate 

because it was not “germane” to the later asserted ground. Andrews, 302 U.S. at 524. 

Other circuits have also recognized this exception.16 Our predecessor court has

also recognized this doctrine. In Addressograph, for example, the Court of Claims held 

that an amendment filed outside the limitations period was “proper and germane” 

because investigation of the merits of the original claim “would have necessarily 

involved a consideration of [the facts the amendment depended on].” AddressographMultigraph Corp. v. United States, 78 F. Supp. 111, 122-23 (Ct. Cl. 1948). The 

amendment “merely made more definite the matters already within the knowledge of the 

Commissioner, which in the course of his investigation he actually did ascertain.” Id. 

 16 See, e.g., United States v. Ideal Basic Indus., Inc., 404 F.2d 122, 124 

(10th Cir. 1968) (permitting amendment where “’facts upon which the amendment is

based would necessarily have been ascertained by the commissioner in determining the 

merits of the original claim’”) (quoting Pink v. United States, 105 F.2d 183, 187 (2d Cir. 

1939)); Pink, 105 F.2d 183, 187 (citing Bemis Bros. Bag, 289 U.S. 28); see also United

States v. Henderson Clay Prods., 324 F.2d 7, 18 (5th Cir. 1963) (limitations requirement 

satisfied for refund claim based on erroneous computation of depletion deduction where 

amended claim “assert[ed] no other ground for recovery than its original” because 

“[b]oth are based upon 114(b)(4)(B), and the amended complaint merely takes account

of a definitive construction of that subsection which was handed down between the date 

of the claims and the date of trial.”); 113 Am. Law Reports 1291 sec. II(e) (1938 & supp. 

05-5014 23
Similarly, in Consolidated Coppermines the court observed that “[w]here the 

amendment is inconsistent with the former claim, or has injected new and unrelated 

matter, we have not allowed it, but where it is germane to the original claim and sets up 

matter discovered in the course of the investigation of the original one, we have allowed 

it.” 296 F.2d at 745. 

Here Computervision’s interest suspension claim as to non-DISC issues cannot 

benefit from the germaneness doctrine for two separate reasons. First, the amended 

claim was not in fact germane to the original claim. The original claim did not merely 

claim an identical amount under a different theory. It claimed a different amount under 

a different theory. Moreover, as the Court of Federal Claims concluded, “the interest 

suspension relief that plaintiff is seeking is not a necessary step in completing the 

interest computation that was explicitly placed at issue in the Original Refund 

Claim . . . .” Computervision, 62 Fed. Cl. at 319 (internal quotation marks omitted). The 

IRS did not discover the interest suspension claim as a result of its investigation of the 

original claim, but rather as a result of Computervision’s May 2, 2000, letter raising the 

interest netting issue. Indeed, Computervision admitted that even as of late 1999, it 

was unaware that an interest suspension claim was available. The IRS consideration of 

the claim “was simply a mistake.” Id. at 321 n.24. The determination of the interest 

attributable to the DISC deficiency did not require the IRS to compute non-DISC interest 

under the interest suspension theory. Even if the IRS possessed the facts necessary to 

make this computation, “it is not enough that somewhere under the Commissioner's roof 

is the information which might enable him to pass on a claim for refund.” Angelus

 

2006); 15 Mertens Law of Federal Income Taxation § 58:38 (1991 & supp. 2006). 

05-5014 24
Milling, 325 U.S. at 299 (rejecting argument that a taxpayer’s refund claim, together with 

the refund claim of another taxpayer, supplied the IRS with the information needed to 

determine the merits of an untimely claim).17

Second, as the Court of Federal Claims held here, the formal amendment was

itself filed too late. Computervision, 62 Fed. Cl. at 328-29. The formal amendment, if 

filed after the expiration of the limitations period, must be filed while the original claim is 

still being considered by the IRS. This requirement “is designed both to prevent 

surprise and to [permit] . . . an administrative investigation and determination.” Union 

Pacific R.R., 389 F.2d at 442. Thus an amendment is ineffective if filed after the original 

claim has either been allowed or disallowed by the IRS. For example, in Union Pacific, 

the Court of Claims concluded that “[t]he disposition of a taxpayer’s refund claim by 

allowance of the amount requested in full, however, precludes an amendment asserting 

an additional amount after the expiration of the statutory period for refund.” Id. at 447 

(emphasis added). So too in Allstate Insurance Co. v. United States, the Court of 

Claims held that “[i]t is a rule of long standing that once a refund claim has been 

disallowed, it is not subject to amendment.” 550 F.2d 629, 633 (emphasis added); see 

also 15 Mertens Law of Federal Income Taxation § 58:38 (“Although amendments to a 

properly filed claim can be made even though the statutory period for filing a claim has

expired, the amendment must be germane, and must be presented before the original

claim is resolved.”); Memphis Cotton, 288 US at 72 (observing that if “at the time of [the] 

 17 See also Andrews, 302 U.S. at 524 (“[A] claim which demands relief upon 

one asserted fact situation, and asks an investigation of the elements appropriate to the 

requested relief, cannot be amended to discard that basis and invoke action requiring 

examination of other matters not germane to the first claim.”). 

05-5014 25
amendment the claim had been finally rejected,” then “the proceeding [had] thereby 

ended” and the amendment “was too late”). 

The same rule necessarily applies where the taxpayer elects to terminate the

IRS’s jurisdiction by filing a suit for refund. While the taxpayer has the right to file a 

refund suit if the IRS has not acted on the claim for six months, the IRS’s jurisdiction 

over the claim necessarily terminates on the date a refund suit is filed. See Exec. Order 

No. 6166, § 5 (June 10, 1933), reprinted in 5 U.S.C. § 901 (2000).18 The IRS no longer

has the authority to resolve the claim, and therefore is without power to “allow” or

“disallow” it. 

We recognize that, as the taxpayer urges, two of our sister circuits have adopted 

a different rule, holding that an amendment is effective for purposes of the 

germaneness doctrine after the IRS has lost jurisdiction over the claim. Mutual 

Assurance Inc. v. United States, 56 F.3d 1353 (11th Cir. 1995); St. Joseph’s Lead Co. 

v. United States, 299 F.2d 348 (2d Cir. 1962) (finding amendment filed after 

commencement of suit was timely). Thus, for example, the Eleventh Circuit in Mutual 

Assurance quoted the Court of Claims’ decision in Union Pacific holding that the 

amendment could not be filed after the allowance of the original claim, but held that

 18 Section 5 of Executive Order 6166 is entitled “Claims By or Against the 

United States,” and reads as follows: 

As to any case referred to the Department of Justice for prosecution or

defense in the courts, the function of decision whether and in what manner 

to prosecute, or to defend, or to compromise, or to appeal, or to abandon 

prosecution or defense, now exercised by any agency or officer, is

transferred to the Department of Justice. 

Exec. Order No. 6166, § 5 (June 10, 1933), reprinted in 5 U.S.C. § 901 (2000); see also

Computervision, 62 Fed. Cl. at 326 n.26 (citing Exec. Order No. 6166, § 5). 

05-5014 26
“[Union Pacific] is not binding precedent in this circuit.” Mutual Assurance, 56 F.3d at

1357. Unlike the Eleventh Circuit we are, of course, bound by the precedent of the 

Court of Claims. S. Corp. v. United States, 690 F.2d 1368, 1369 (Fed. Cir. 1982) (en 

banc) (the Federal Circuit is bound by decisions of the Court of Claims “announced 

before the close of business on September 30, 1982”). 

In any event it seems to us that the Court of Federal Claims was correct here in 

suggesting the rule adopted by our sister circuits in St. Joseph’s Lead and Mutual 

Assurance is untenable since it would allow amendments submitted after filing the 

refund suit to extend the limitations period indefinitely. Computervision, 62 Fed. Cl. at

328-29. Here Computervision filed its original refund suit in the Court of Federal Claims 

on April 4, 1990, and then filed an amendment with the IRS on April 4, 2002, in which it 

claimed non-DISC interest under the interest suspension theory. Computervision’s

amendment in 2002, 12 years after filing suit and after the IRS’s jurisdiction had been

terminated by the filing of the refund suit, came too late. 

Thus this exception does not apply to Computervision’s claim. 

E 

For the foregoing reasons, Computervision’s interest suspension claim must fail. 

There was no informal claim, and the waiver, general claim and germaneness doctrines 

are also inapplicable. 

II 

The taxpayer also asserts that it was entitled to recovery of the non-DISC interest

under the theory of interest netting. 

Under section 6621(d), the IRS applies a net interest rate of zero to overlapping 

05-5014 27
underpayments and overpayments of tax. Section 6621(d), enacted on July 22, 1998, 

provides: 

Elimination of interest on overlapping periods of tax overpayments and 

underpayments.—To the extent that, for any period, interest is payable 

under subchapter A and allowable under subchapter B on equivalent

underpayments and overpayments by the same taxpayer of tax imposed 

by this title, the net rate of interest under this section on such amounts

shall be zero for such period. 

26 U.S.C. § 6621(d) (2000). Computervision argues that its overpayment for the 1982 

year, which arose on March 15, 1983, the due date of its 1982 return, should be netted 

against the subsequently determined underpayment for 1982. Although the 1982 

overpayment was credited towards subsequent years, it was not needed to pay liability

for those years. Thus, according to Computervision, the overpayment retained its

status as a 1982 overpayment until August 2, 1985, when it was finally refunded. 

The government does not claim that the taxpayer’s failure to file the claim within 

the limitations period is a bar, because the interest netting statute provides for

retroactive relief under certain circumstances. However, the government asserts that 

the doctrine is inapplicable for a number of reasons. We need to address only one 

because we agree with the government that under our decision in Federal National

Mortgage Association v. United States, 379 F.3d 1303 (Fed. Cir. 2004) (“FNMA”), the 

taxpayer has failed to satisfy the requirement for retroactive application of the statute. 

The interest Computervision contests arose prior to the enactment of section 

6621(d). Section 6621(d) applies retroactively only under certain circumstances.19 

Specifically, section 6621(d) is “[s]ubject to any applicable statute of limitation not 

 19 The requirements for retroactive application of interest netting are 

05-5014 28
having expired with regard to either a tax underpayment or a tax overpayment” as of 

July 22, 1998. Pub. L. No. 105-277, § 4002(d), 112 Stat. 2681 (1998), amending Pub. 

L. No. 105-206, § 3301(c)(2), 112 Stat. 741 (1998). In FNMA, we interpreted this 

language to require that the statute of limitations must be open with respect to both the 

underpayment and the overpayment. 

A claim for a refund of paid underpayment interest is barred if not filed within the 

later of three years from the date the return was filed or two years from the date the 

interest was paid. 26 U.S.C. § 6511. The underpayment interest in this case is the 

1982 deficiency interest, which was paid on April 28, 1989. The limitations period for

the underpayment closed two years later, on April 28, 1991 -- several years before the 

July 22, 1998, date specified in section 3301(c)(2). 

A claim for interest from overpayments must be filed within six years after the 

due date of the return that gave rise to the overpayment interest. See 28 U.S.C. § 2401 

(2000). In Computervision’s case, the overpayment limitations periods expired on 

March 15, 1989, for the 1982 tax year; March 15, 1990, for the 1983 tax year; and 

August 2, 1991, for the 1984 tax year. All these periods were closed as of the July 22,

1998, critical date specified in § 3301(c)(2). Computervision’s argument that the 

limitations periods remained open indefinitely while its DISC claim was being litigated is

without merit. 

Thus, as of July 22, 1998, the statute of limitations was closed with respect to 

both underpayment and overpayment interest, and thus Computervision’s claim for

interest netting fails to satisfy the requirements for retroactive application of the statute. 

 

explained in Revenue Procedure 99-43. Rev. Proc. 99-43, 1999-2 C.B. 579. 

05-5014 29
CONCLUSION 

For the foregoing reasons, the judgment of the Court of Federal Claims is 

AFFIRMED. 

COSTS 

No costs. 

05-5014 30