<PAGE>
 
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                                    FORM 10-K


(Mark One)

[X]  ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE
     ACT OF 1934 
     For the fiscal year ended December 31, 1998

[ ]  TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES
     EXCHANGE ACT OF 1934 
     For the transition period from _______________ to _______________


                         Commission file number 0-18301


                             IROQUOIS BANCORP, INC.
             (Exact name of Registrant as specified in its charter)

           New York                                             16-1351101      
(State or other jurisdiction of                              (I.R.S. Employer   
incorporation or organization)                            Identification Number)


115 Genesee Street, Auburn, New York                              13021
(Address of principal executive offices)                         Zip Code

Registrant's telephone number, including area code: (315) 252-9521

Securities registered pursuant to Section 12(b) of the Act: None

Securities registered pursuant to Section 12(g) of the Act:

                          Common Stock, $1.00 par value
                                (Title of Class)


Indicate by check mark whether the Registrant (1) has filed all reports required
to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during
the preceding 12 months (or for such shorter period that the Registrant was
required to file such reports), and (2) has been subject to such filing
requirements for the past 90 days.

Yes _X_        No ___

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405
of Regulation S-K is not contained herein, and will not be contained, to the
best of Registrant's knowledge, in definitive proxy or information statements
incorporated by reference in Part III of this Form 10-K or any amendment to this
Form 10-K. |_|
<PAGE>
 
The aggregate market value of the shares of Registrant's voting stock, its
Common Stock, held by non-affiliates of Registrant as of February 26, 1999 was
$38,522,317 based upon the closing sale price of $21.75 per share of Common
Stock on that date, as reported by the NASDAQ Stock Market.

The number of shares outstanding of Registrant's Common Stock as of February 26,
1999 was 2,426,880.


                       Documents Incorporated by Reference

Portions of the Registrant's Annual Report to Shareholders for the fiscal year
ended December 31, 1998 are incorporated by reference into Part I and II.

Portions of the Registrant's Definitive Proxy Statement relating to the Annual
Meeting of Shareholders to be held April 29, 1999 are incorporated by reference
into Part III.

     This annual report contains certain "forward-looking statements" covered by
the "safe harbor" provisions of the Private Securities Litigation Reform Act of
1995. The Company is making this statement for the express purpose of availing
itself of the safe harbor protection with respect to any and all of such
forward-looking statements, including those contained in Management's Discussion
and Analysis which describe future plans or strategies and include the Company's
expectations of future financial results. The words "believe," "expect,"
"anticipate," "estimate," "project," and similar expressions identify
forward-looking statements. The Company's ability to predict results or the
effect of future plans or strategies is inherently uncertain. Factors that could
affect actual results include interest rate trends, the general economic climate
in the Company's market areas or in the country as a whole, loan delinquency
rates, and changes in federal and state regulation. These factors should be
considered in evaluating the forward-looking statements, and undue reliance
should not be placed on such statements.




                                       2
<PAGE>
 
                                     PART I

Item 1. Description of Business

General

     Iroquois Bancorp, Inc. (the "Company"), a New York corporation, is a bank
holding company that operates two wholly-owned financial institution
subsidiaries: Cayuga Bank , a New York state-chartered commercial bank and trust
company with its principal offices located in Auburn, New York and The Homestead
Savings FA ("Homestead Savings"), a federally chartered savings association with
its principal offices located in Utica, New York. Prior to January 1, 1997, the
Company was a thrift holding company and Cayuga Bank was a New York state
chartered savings bank. The Company became a bank holding company in connection
with the change in Cayuga Bank's charter from a savings bank to a commercial
bank under New York state law. Cayuga Bank and Homestead Savings are sometimes
referred to herein as the "member banks."

Description of business

     The Company, through its member banks and their respective subsidiaries
(collectively, the "Subsidiaries"), is engaged solely in the business of
providing financial services to consumers and businesses. The Company caters to
the particular needs of its market areas through the Subsidiaries, offering a
broad range of financial products and services. Loan products offered by the
Company include mortgages, home equity loans and lines of credit, consumer
installment loans, credit cards, student loans, and commercial loans; deposit
products include savings, checking and time deposits, money market accounts, a
range of deposits for municipalities or other public corporations, and mortgage
escrow accounts. The Company also provides insurance agency services, investment
brokerage services, trust services and safe deposit facilities.

     The business of the Company is more fully described in Management's
Discussion and Analysis at pages 5 through 22 of the Company's Annual Report to
Shareholders for the fiscal year ended December 31, 1998 (the "1998 Annual
Report to Shareholders"), incorporated herein by reference to Exhibit (13)
hereto.

Market Area

     The Company's market area primarily covers the Central New York counties of
Cayuga, Oswego and Oneida. Cayuga and Oswego counties are part of the Syracuse
MSA, which also includes Onondaga and Madison counties. Oneida County is part of
the Utica MSA, which also includes Herkimer County. The Company's residential
mortgage lending extends to Monroe County, part of the Rochester MSA, and parts
of Seneca and Onondaga counties through a broker network, as well as to Old
Forge and Lake Placid, NY, through loan production offices.

     A recent estimate by the U.S. Census Bureau shows the upstate New York
population decreasing by 24,965 people or .4% from July 1997 to July 1998.
Cayuga County population declined by .5%, slightly more than the upstate
average. Oneida County led the state in population decline from 1990 to 1997
with 7.0%, or 17,649 people leaving the county. The Syracuse area lost 4.5%, or
33,445 people during the same period.


                                       3
<PAGE>
 
     The percentage of population over age 60 increased by 3% for Cayuga County,
and 6% for both Oswego and Oneida counties from the period 1980 to 1990. Nearly
one-third of the total population in these counties exceeds 60 years of age.
These statistics seem to follow a national trend of people living longer. The
Company intends to focus on this market segment with products and services
designed to accommodate an older population. These include relationship
accounts, trust and investment services and products for meeting housing needs
of the elderly through innovative mortgage programs.

     In 1998, the Central New York economy grew twice as fast as estimated and
faster than any time since 1990. Job growth for 1998 in the Syracuse MSA was
1.2%, compared to a national average of 2.6%. Service sector jobs grew the most,
adding 1,600 jobs. Manufacturing was second with job growth of 1,300 jobs. Every
major industry added jobs except for retailing which lost 700 jobs.

     The unemployment rate for the Syracuse MSA was 3.6% for December 1998 down
from 4.5% a year earlier. The unemployment rate for New York State for December
1998 was 5.1% while the national rate was 4.3%. The December year over year
unemployment rate for Cayuga County improved from 5.6% in 1997 to 5.2% in 1998.
Oneida County improved from 4.7% to 3.7% while Oswego County improved from 6.8%
to 5.7% The unemployment rate for the Rochester MSA improved from 4.0% to 3.6%.
The Utica MSA improved from 5.2% to 4.1%.

     The Central New York housing market improved during 1998. Sales in the
Syracuse MSA were 18% higher while the median sales price increased 1.4%.
Nationally, sales were up 16% with a comparable percentage increase in median
price. The backlog of unsold homes has declined but remains relatively high in
the Company's primary market areas. The Rochester area housing market remains
the strongest market in the Upstate NY area exhibiting continued growth in
housing sales and a less than 2.6 month supply of unsold homes.

Competition

     Because the primary business of the Company is the ongoing business of its
Subsidiaries, the competitive conditions faced by the Company are primarily
those of the member banks as financial institutions in their respective
geographic markets. Within their respective market areas, the member banks
encounter intense competition from other financial institutions offering
comparable products. These competitors include commercial banks, savings banks,
savings and loan associations, and credit unions. Competition for the broader
range of financial services provided by the Subsidiaries also comes from
non-banking entities such as personal loan companies, sales finance companies,
leasing companies, securities brokers and dealers, insurance companies, mortgage
companies, and money market and mutual fund companies.

     To differentiate itself from the competition in its market areas, the
Company places strong emphasis on providing customers with highly personalized
service and products tailored to the needs of its retail and commercial
customers. The Subsidiaries also utilize personal sales calls, convenient hours
and locations, and relationship-based products and services to enhance customer
retention and loyalty.

     In addition to competition for financial services, the Company itself faces
competition for acquisition of other banking institutions or their branches.
Numerous banks and financial institutions in the Company's market areas are
pursuing acquisition strategies and have formed holding companies for the same
reasons as the Company.


                                       4
<PAGE>
 
Statistical Disclosure by Bank Holding Companies

I.   Distribution of Assets, Liabilities and Stockholders' Equity; Interest
     Rates and Interest Differential

     Information required by this section of Securities Act Industry Guide 3, or
     Exchange Act Industry Guide 3 (Guide 3), is presented in the Registrant's
     1998 Annual Report to Shareholders in Management's Discussion and Analysis
     on page 7 in Table 1 - Net Interest Income Analysis, and on page 8 in Table
     2 - Rate/Volume Analysis, which Tables 1 and 2 are incorporated herein by
     reference.

II.  Investment Portfolio

     Information required by this section of Guide 3 is presented in the
     Registrant's 1998 Annual Report to Shareholders in Management's Discussion
     and Analysis on page 15 in Table 6 - Securities and on page 16 in Table 7 -
     Maturity Schedule of Securities, which Tables 6 and 7 are incorporated
     herein by reference.

III. Loan Portfolio

     A.   Composition of Loan Portfolio

          Information required by this section of Guide 3 is presented in the
          Registrant's 1998 Annual Report to Shareholders in Management's
          Discussion and Analysis on page 10 in Table 3 - Summary of the Loan
          Portfolio, which Table 3 is incorporated herein by reference.

     B.   Maturities and Sensitivities of Loans to Changes in Interest Rates

          Information required by this section of Guide 3 is presented in
          Registrant's 1998 Annual Report to Shareholders in Management's
          Discussion and Analysis on page 10 in the table entitled Selected Loan
          Maturity and Interest Rate Sensitivity, which Table is incorporated
          herein by reference.

     C.   1.   Risk Elements

               Information required by this section of Guide 3 is presented in
               the Registrant's 1998 Annual Report to Shareholders in
               Management's Discussion and Analysis on page 14 in Table 5 -
               Summary of Non-Performing Assets, which Table 5 is incorporated
               herein by reference.

          2.   Potential Problem Loans

               Information required by this section of Guide 3 is presented in
               the Registrant's 1998 Annual Report to Shareholders in
               Management's Discussion and Analysis on pages 13 through 14, in
               the discussion under the caption Non-Performing Assets, which
               discussion is incorporated herein by reference.


                                       5
<PAGE>
 
          3.   Foreign Outstandings

               The Company does not make loans to foreign companies and, at
               December 31, 1998, 1997 and 1996, there were no foreign loans
               outstanding.

          4.   Loan Concentrations

               Information required by this section of Guide 3 is presented in
               the Registrant's 1998 Annual Report to Shareholders on page 43 in
               note (16) of the Notes to Consolidated Financial Statements
               relating to Commitments and Contingencies, which note (16) is
               incorporated herein by reference.

IV.  Summary of Loan Loss Experience

     A.   Analysis of the Allowance for Loan Losses

          Information required by this section of Guide 3 is presented in the
          Registrant's 1998 Annual Report to Shareholders in Management's
          Discussion and Analysis on page 13 in Table 4 - Allowance for Loan
          Losses, in the discussion on page 12 under the caption reference.
          Allowance for Loan Losses and in the discussion on pages 13 through 14
          under the caption Non-Performing Assets, which Table 4 and which
          discussions are incorporated herein by reference.

     B.   Allocation of the Allowance for Loan Losses

          Information required by this section of Guide 3 is presented in the
          Registrant's 1998 Annual Report to Shareholders in Management's
          Discussion and Analysis on page 13 in that portion of Table 4 -
          Allowance for Loan Losses under the separate table heading Allocation
          of Allowance for Loan Losses at December 31, which portion of Table 4
          is incorporated herein by reference.

V.   Deposits

     Information required by this section of Guide 3 is presented in the
     Registrant's 1998 Annual Report to Shareholders in Management's Discussion
     and Analysis on page 7 in Table 1 - Net Interest Income Analysis, on page
     17 in Table 8 - Deposits and on page 17 in Table 9 - Maturities of Time
     Deposits - $100,000 and Over, which Tables 1, 8 and 9 are incorporated
     herein by reference.

VI.  Return on Equity and Assets

     Information required by this section of Guide 3 is presented in the
     Registrant's 1998 Annual Report to Shareholders on page 4 in the table
     entitled Selected Consolidated Financial Data, which Table is incorporated
     herein by reference.

VII. Short-Term Borrowings

     Information required by this section of Guide 3 is presented in the
     Registrant's 1998 Annual Report to Shareholders on page 36 in note (7) of
     the Notes to Consolidated Financial Statements


                                       6
<PAGE>
 
     relating to Borrowings, in that portion of the table therein on information
     related to the Federal Home Loan Bank Line of Credit at December 31, 1998
     and 1997 and in the discussion therein under the caption Line of Credit and
     Term Advances, which tabular information and discussions are incorporated
     herein by reference.

Employees

     At December 31, 1998, the Company and its Subsidiaries had 176 full-time
and 36 part-time employees. The Company and its Subsidiaries provide a variety
of benefit programs including group life, health, accident and other insurance
benefits, and retirement and stock ownership plans.

Regulation and Supervision

     The earnings of the member banks, and therefore the earnings of the
Company, are affected by policies of regulatory authorities, most significantly
the Board of Governors of the Federal Reserve System (the "FRB") which
implements policies to influence interest rates and the supply of money and
credit in the banking system. The FRB's monetary policies strongly influence the
behavior of interest rates and can have a significant effect on the operating
results of commercial banks, primarily through the FRB's policies that have a
direct impact on interest rates. The effects of various FRB policies on future
business and earnings of the Company cannot be predicted, nor can the nature or
extent of any effects of possible future governmental controls, legislative or
regulatory changes that may be implemented by the FRB or any of the other
regulatory agencies with jurisdiction over the Company or its Subsidiaries.

     As sole shareholder of Cayuga Bank, under federal law the Company is a bank
holding company subject to the jurisdiction of the FRB. The Company also falls
within the definition of a thrift holding company as sole shareholder of
Homestead Savings, under the jurisdiction of the Office of Thrift Supervision
("OTS"). Under the provisions of the Economic Growth and Regulatory Paperwork
Reduction Act of 1996 ("EGRPRA"), the OTS adopted rules applicable to holding
companies that qualify as both a bank and thrift holding company, and the OTS no
longer supervises a holding company that controls both a bank and a savings
association if it is registered with the FRB. Accordingly, under federal law,
the Company files all reports with and is subject to regulation, examination,
and supervision solely by the FRB even though it continues to own a savings
association. OTS, however, continues to be the primary regulatory authority for
Homestead Savings, the Company's wholly-owned savings association subsidiary.

     The Company also has been and continues to be a bank holding company for
purposes of state law and, as such, is subject to regulation, examination, and
supervision by the New York State Banking Department.

     Cayuga Bank operates as a commercial bank, chartered as a New York State
trust company, and is subject to regulation, supervision and examination by the
New York State Banking Department as its primary regulatory authority and by the
Federal Deposit Insurance Corporation ("FDIC"). Homestead Savings is subject to
regulation, supervision and examination by the OTS as its primary regulatory
authority. Cayuga Bank's deposits are insured by the FDIC Bank Insurance Fund
("BIF") and Homestead Savings' deposits are insured by the FDIC Savings
Association Insurance Fund ("SAIF"). Each of the financial institutions is
subject to assessment of insurance premiums as the FDIC may require from time to
time to assure that the BIF and SAIF have adequate reserves. During the last
year, Cayuga Bank, as a well-capitalized institution insured by BIF, paid an
assessment of $0.012 per $100 of qualifying deposits and Homestead Savings, as a
well-capitalized SAIF-insured institution, paid $0.06 per $100 of qualifying
deposits. FDIC deposit insurance coverage under the respective BIF and SAIF is
generally in amounts up


                                       7
<PAGE>
 
to $100,000 per depositor. The FDIC has the power to terminate insured status or
to suspend it temporarily under special conditions.

     The FRB has adopted minimum capital ratios and guidelines for assessing the
adequacy of capital of bank holding companies. The minimum capital ratios
consist of a risk-based measure, a leverage ratio and a Tier 1 leverage ratio.
Under the risk-based measure, a bank holding company must have a minimum ratio
of qualifying total capital to risk-weighted assets equal to 8%, of which at
least 4% must be in the form of Tier 1 capital. Qualifying total capital is
calculated by adding Tier 1 capital and Tier 2 capital. The risk-based capital
ratio, calculated by dividing qualifying capital by risk-weighted assets, also
incorporates capital charges for certain market risks. The leverage measure of
capital is based on two components, a minimum level of primary capital to total
assets of 5.5% and a minimum level of total capital to total assets of 6.0%. The
Tier 1 leverage ratio requires the ratio of Tier 1 capital to total assets be at
least 3%, for strong bank holding companies and those that have implemented a
risk-based capital measurement that includes market risk factors. All other
holding companies must have a minimum 4% Tier 1 leverage ratio, and an even
higher ratio may be imposed on weaker organizations. At December 31, 1998, the
Company's capital ratios were in excess of the minimum requirements.

     The FRB also places bank holding companies into various categories based
upon these measures of capital adequacy, of which the highest level is "well
capitalized." A bank holding company is considered well capitalized if it
maintains a risk-based capital ratio of 10% or greater and a Tier 1 risk-based
capital ratio of 6% or greater, and if the bank holding company is not subject
to any written agreement, order or similar directive issued by FRB for
maintaining capital levels. Under EGRPRA, a bank holding company that is deemed
to be well-capitalized may engage in permissible non-banking activities without
prior approval from the FRB. Based on the Company's calculation of its capital
ratios, the Company qualifies as a well capitalized bank holding company.

     Both of the financial institution subsidiaries of the Company are also
subject to specific capital requirements of their respective regulators. Cayuga
Bank is subject to FDIC guidelines which require Tier 1 capital of at least 3%
of total assets, and 1% to 2% higher depending upon the bank's financial
condition and growth strategy. The FDIC risk-based capital guidelines require
that the ratio of total capital to risk-weighted assets must be at least 8%,
with a minimum of 4% in Tier 1 capital. Homestead Savings is subject to the
capital adequacy guidelines of the OTS, which require tangible capital of at
least 1.5% of total assets, core capital of at least 3% of total assets, and
minimum risk-based capital of 8% of risk-weighted assets. Both subsidiaries have
in excess of these capital requirements.

     For supervisory purposes, each of the federal bank regulatory agencies have
promulgated regulations establishing five categories, ranging from
well-capitalized to critically under-capitalized, depending upon the
institution's capital and other factors. Capital adequacy provisions that apply
to both Cayuga Bank and Homestead Savings under guidelines adopted by all
federal banking regulatory agencies also require market risk measures to be
included in risk-based capital standards.

     The Riegle-Neal Interstate Banking Efficiency Act of 1994 permits bank
holding companies and banks to engage in transactions involving interstate
acquisitions and mergers if the holding company and banking institution are
adequately capitalized and managed. The FRB imposes restrictions, however, on
the acquisition by the Company of more than 5% of the voting shares of any bank
or other bank holding company. The extent to and terms on which full interstate
branching and certain other actions authorized under the Riegle-Neal Act are
implemented will depend on the actions of entities other than the Company and
its member banks, including the legislatures of the various states. Further
developments by state and federal authorities, including legislation, with
respect to matters covered by the Riegle-Neal Act reasonably can be anticipated
to occur in the future. 


                                       8
<PAGE>
 
     Under the Community Reinvestment Act of 1977 ("CRA"), the federal
regulatory agencies are required to assess whether the holding company or
institutions are meeting the credit needs of the communities served. All bank
regulatory agencies take CRA ratings into consideration in connection with any
application for mergers, consolidations, including applications for acquiring
branch offices of operating institutions. New York State Banking Department
regulations impose similar requirements with respect to the CRA.

     Cayuga Bank and Homestead Savings are also subject to certain FRB
regulations for the maintenance of reserves in cash or in non-interest bearing
accounts, the effect of which is to increase their cost of funds. Cayuga Bank is
also subject to comprehensive New York state regulation, including limitations
on the amount of dividends that may be paid to Iroquois as its sole shareholder.

     New banking legislation related to bank holding companies and their
subsidiaries has been under consideration by Congressional committees on a
regular basis in recent years. The likelihood of success of any such legislation
and the effect, if any, of such legislation on the Company and its Subsidiaries
cannot be predicted.


                                       9
<PAGE>
 
Item 2. Properties

     The Company's properties are all located in Central New York State. Six
banking office facilities are utilized by Cayuga Bank: three in Auburn, one in
Weedsport, one in Moravia, and one in Lacona, all of which are owned. The
Company has two offices in Utica, one office in Waterville, and one office in
Clinton, that are all owned and utilized as banking offices by Homestead
Savings. The Company also leases space in Freedom Mall, Rome, New York for use
by Homestead Savings. The lease was extended upon its expiration in June, 1998
on a month-to-month basis. Homestead Savings is currently looking for a new
location for this facility. All of these properties are in generally good
condition and appropriate for their intended use.

Item 3. Legal Proceedings

     The Company is not involved in any pending legal proceedings, other than
routine legal proceedings undertaken in the ordinary course of business or legal
proceedings that, in the opinion of the management after consultation with
counsel, if determined adversely, would not have a material effect on the
consolidated financial condition or results of operations of the Company.

Item 4. Submission of Matters to a Vote of Stockholders

     NONE


                              * * * * * * * * * * *


                      EXECUTIVE OFFICERS OF THE REGISTRANT
                      ------------------------------------
<TABLE>
<CAPTION>
         Name                  Age                Title
         ----                  ---                -----
                             
<S>                            <C>       <C>                                   
Richard D. Callahan            56        President and Chief Executive Officer
Marianne R. O'Connor           44        Treasurer and Chief Financial Officer
Richard J. Notebaert, Jr.      55        Vice President
W. Anthony Shay, Jr.           56        Vice President-Operations
</TABLE>

     All of the foregoing executive officers were elected by the Company's board
of directors at its first board meeting in January for the fiscal year. Each
such executive officer was so elected to serve the Company, in addition to the
officer's primary duties as an executive officer of Cayuga Bank or Homestead
Savings, for a term of one year and until his or her successor is duly elected
and qualified at the first meeting of the board of directors held in January of
each fiscal year.

     Richard D. Callahan, President and Chief Executive Officer, joined both the
Company and Cayuga Bank in 1994. Prior to that time, he was Regional Executive
Vice President, Regional President, and Senior Executive Vice President of
Operations and Marketing, in that order, for Marine Midland Bank from 1983 to
1993, after 18 years of prior banking experience.


                                       10
<PAGE>
 
     Marianne R. O'Connor, Treasurer and Chief Financial Officer, joined Cayuga
Bank as manager of the Loan Servicing Department in 1979, subsequently served as
Assistant Comptroller, and was promoted to Treasurer in 1985 and to Chief
Financial Officer in 1988.


     Richard J. Notebaert, Jr., Vice President, joined Homestead Savings in
February 1990 as Executive Vice President, and was promoted to President and
Chief Executive Officer of Homestead in 1992. Prior to that time, he had been
Executive Vice President of Monroe Savings Bank for 14 years.


     W. Anthony Shay, Jr., Vice President-Operations, joined Cayuga Bank in
February, 1995 as Vice President. Prior to that time, he was Senior Vice
President Operations Support, Senior Vice President Processing Services Group,
Senior Vice President and Regional Executive, and held other various positions
with Marine Midland Bank from 1964 to 1994.



                                       11
<PAGE>
 
                                     PART II


Item 5. Market for Registrant's Common Equity and Related Stockholder Matters

     Reference is made to the information on page 46 of the Company's 1998
Annual Report to Shareholders, incorporated herein by reference to Exhibit (13)
hereto.

Item 6. Selected Financial Data

     Reference is made to Selected Consolidated Financial Data on page 4 of the
Company's 1998 Annual Report to Shareholders, incorporated herein by reference
to Exhibit (13) hereto.

Item 7. Management's Discussion and Analysis of Financial Condition and Results
        of Operations

     Reference is made to Management's Discussion and Analysis in the Company's
1998 Annual Report to Shareholders on pages 5 through 22 thereof, incorporated
herein by reference to Exhibit (13) hereto.

Item 7A. Quantitative and Qualitative Disclosures About Market Risk

     Reference is made to the discussion under the caption Market Risk and
Interest Rate Risk Management on pages 18 through 20 and to Table 10 - Net
Portfolio Value Analysis and Table 11 - Interest Rate Sensitivity Table on page
20 of Management's Discussion and Analysis in the Company's 1998 Annual Report
to Shareholders, which discussion and Tables 10 and 11 are incorporated herein
by reference to Exhibit (13) hereto.

Item 8. Financial Statements and Supplementary Data

     The consolidated financial statements of the Company, together with the
report thereon of its independent auditors, included in the 1998 Annual Report
to Shareholders on pages 24 through 45 thereof, along with the Unaudited
Summarized Quarterly Financial Information on page 46 thereof, are incorporated
herein by reference to Exhibit (13) hereto. The financial statements of the
Iroquois Bancorp 401(k) Savings Plan, together with the report thereon of its
independent auditors, as required by Rule 15d-21 pursuant to Section 15(d) of
the Securities Exchange Act of 1934, as amended, are incorporated herein by
reference to Exhibit (99) hereto.


Item 9. Changes in and Disagreements with Accountants on Accounting and
        Financial Disclosure

     None.


                                       12
<PAGE>
 
                                    PART III


Item 10. Directors and Executive Officers of the Registrant

     (a)  Identification of directors.

          Reference is made to pages 4 and 5 under the caption ELECTION OF
     DIRECTORS in the Company's Definitive Proxy Statement relating to its
     Annual Meeting of Shareholders to be held on April 29, 1999 (the "Proxy
     Statement"), incorporated herein by reference.

     (b)  Identification of executive officers.

          The information pertaining to the Company's executive officers is
     included in Part I of this Annual Report on Form 10-K following Item 4
     hereof as permitted by Instruction 3 to Item 401(b) of Regulation S-K.

     (c)  Family relationships.

          There are no family relationships between any director, executive
     officer, or any person nominated or chosen by the Company to become a
     director or executive officer. Officers of the Company serve for a term of
     office from the date of election to the next annual meeting of the board of
     directors and until their respective successors are elected and qualified,
     except in the case of death, resignation, or removal. There are no
     arrangements or understandings with any other person pursuant to which any
     director or executive officer was elected to such position.

     (d)  Compliance with Section 16(a) of the Exchange Act

          Reference is made to the information under the caption COMPLIANCE WITH
     SECTION 16(a) OF THE SECURITIES EXCHANGE ACT OF 1934 in the Company's Proxy
     Statement on page 4 thereof, incorporated herein by reference.

Item 11. Executive Compensation

     Reference is made to the information under the caption EXECUTIVE
COMPENSATION on pages 7 through 14 of the Company's Proxy Statement,
incorporated herein by reference.

Item 12. Security Ownership of Certain Beneficial Owners and Management

     Reference is made to the information under the caption STOCK OWNERSHIP OF
CERTAIN BENEFICIAL OWNERS AND MANAGEMENT on pages 2 and 3 of the Company's Proxy
Statement, incorporated herein by reference. There are no arrangements known to
the Company, including any pledge by any person of securities of the Company,
the operation of which may, at a subsequent date, result in a change of control
of the Company.

Item 13. Certain Relationships and Related Transactions

     Reference is made to the information under the caption CERTAIN TRANSACTIONS
on page 16 of the Company's Proxy Statement, incorporated herein by reference.



                                       13
<PAGE>
 
                                     PART IV


Item 14. Exhibits, Financial Statement Schedules, and Reports on Form 8-K

(a)  (1)  Financial Statements and Report of Independent Auditors. The following
          consolidated financial statements and reports of the Company are
          incorporated in this Annual Report on Form 10-K by reference to the
          1998 Annual Report to Shareholders annexed hereto as Exhibit (13):

               Report of Independent Auditors.

               Consolidated Balance Sheets as of December 31, 1998 and 1997.

               Consolidated Statements of Income for each of the years in the
               three-year period ended December 31, 1998.

               Consolidated Statements of Cash Flows for each of the years in
               the three-year period ended December 31, 1998.

               Consolidated Statements of Shareholders' Equity and Comprehensive
               Income for each of the years in the three-year period ended
               December 31, 1998.

               Notes to Consolidated Financial Statements.

     (2)  Financial Statement Schedules. All financial statement schedules have
          been omitted as they are not applicable, not required, or the
          information is included in the consolidated financial statements or
          notes thereto.

     (3)  Exhibits. The following exhibits are filed herewith or have been
          previously filed with the Securities and Exchange Commission, as
          noted, and numbered in accordance with Item 601 of Regulation S-K:

          Number                        Description
          ------                        -----------

          3(A)(I)   Restated Certificate of Incorporation of Registrant,
                    incorporated by reference to the Registrant's Registration
                    Statement on Form 8-A (No. 0-18301), filed with the
                    Commission on November 12, 1991, wherein such exhibit is
                    designated Exhibit 2(I)(2)(a).


                                       14
<PAGE>
 
          3(A)(II)  Certificate of Amendment of the Certificate of Incorporation
                    of Registrant, incorporated by references to the
                    Registrant's Quarterly Report on Form 10-Q for the quarter
                    ended September 30, 1996, filed with the Commission on
                    November 7, 1996, wherein such exhibit was designated
                    Exhibit 3.1.

          3(B)      Bylaws of Registrant, incorporated by reference to the
                    Registrant's Quarterly Report on Form 10-Q for the quarter
                    ended September 30, 1995, filed with the Commission on
                    November 13, 1995, wherein such exhibit is designated
                    Exhibit 3(ii).

                                   ***********

                    Compensatory Plans or Arrangements

          10(A)     Employment Agreement with Richard D. Callahan, incorporated
                    by reference to Registrant's Quarterly Report on Form 10-Q
                    for the quarter ended March 31, 1997, filed with the
                    Commission on May 14, 1997, wherein such exhibit is
                    designated 10(A).

          10(B)     Employment Agreement with Marianne R. O'Connor, incorporated
                    by reference to Registrant's Quarterly Report on Form 10-Q
                    for the quarter ended March 31, 1997, filed with the
                    Commission on May 14, 1997, wherein such exhibit is
                    designated 10(C).

          10(C)     Employment Agreement with Richard J. Notebaert, Jr.,
                    incorporated by reference to Registrant's Quarterly Report
                    on Form 10-Q for the quarter ended March 31, 1997, filed
                    with the Commission on May 14, 1997, wherein such exhibit is
                    designated 10(B).

          10(D)     Employment Agreement with Henry M. O'Reilly, incorporated by
                    reference to Registrant's Quarterly Report on Form 10-Q for
                    the quarter ended March 31, 1997, filed with the Commission
                    on May 14, 1997, wherein such exhibit is designated 10(D).

          10(E)     Employment Agreement with W. Anthony Shay, Jr., incorporated
                    by reference to Registrant's Quarterly Report on form 10-Q
                    for the quarter ended March 31, 1997, filed with the
                    Commission on May 14, 1997, wherein such exhibit is
                    designated Exhibit 10(D).

          10(F)     Amended and Restated 1988 Stock Option Plan, incorporated by
                    reference to Registrant's Registration Statement on Form S-8
                    (No. 33-94214), filed with the Commission on June 29, 1995,
                    wherein such exhibit is designated Exhibit 99.


                                       15
<PAGE>
 
          10(G)     1996 Stock Option Plan, incorporated by reference to
                    Registrant's Registration Statement on Form S-8
                    (No.333-10063), filed with the Commission on August 13,
                    1996, wherein such exhibit is designated Exhibit 99.

          10(H)     Stock Purchase Incentive Program, incorporated by reference
                    to Registrant's Annual Report on form 10-K for the fiscal
                    year ended December 31, 1996, filed with the Commission on
                    March 27, 1997, wherein such exhibit is designated Exhibit
                    10(I).

          10(I)     Description of Iroquois Bancorp, Inc. Annual Management
                    Incentive Plan.

          10(J)     Retirement Benefits Agreement with Richard D. Callahan,
                    incorporated by reference to Registrant's Annual Report on
                    Form 10-K for the fiscal year ended December 31, 1994, filed
                    with the Commission on March 29, 1995, wherein such exhibit
                    is designated 10(L).

          10(K)     Separation Agreement with James H. Paul, incorporated by
                    reference to Registrant's Quarterly Report on 10-Q for the
                    quarter ended March 31, 1997, filed with the Commission on
                    May 14, 1997, wherein such exhibit is designated Exhibit
                    10(F).

                                  ************

          13        Annual Report to Shareholders for Fiscal Year Ended December
                    31, 1998.

          21        List of Subsidiaries.

          23(A)     Consent of KPMG LLP with respect to the Annual Report on
                    Form 10-K for the Fiscal Year Ended December 31, 1998.

          23(B)     Consent of Fagliarone Group P.C. with respect to Exhibit 99
                    of the Annual Report on Form 10-K for the Fiscal Year Ended
                    December 31, 1998.

          24        Power of Attorney, included with the Signature Page of this
                    Annual Report on Form 10-K.

          99        Iroquois Bancorp, Inc. 401(k) Savings Plan Financial
                    Statements and Schedules for the Fiscal Years Ended December
                    31, 1998 and 1997, together with Independent Auditors'
                    Report Thereon of Fagliarone Group P.C. for the year ended
                    December 31, 1998 and KPMG LLP for the year ended December
                    31, 1997.


                                       16
<PAGE>
 
                                   SIGNATURES

     Pursuant to the requirements of Section 13 or 15(d) of the Securities
Exchange Act of 1934, the Registrant has duly caused this report to be signed on
its behalf by the undersigned, thereunto duly authorized in the City of Auburn,
County of Cayuga, and State of New York on March 16, 1999.

                                      IROQUOIS BANCORP, INC.


                                      By: /s/Richard D. Callahan                
                                          -------------------------------------
                                          Richard D. Callahan
                                          President and Chief Executive Officer


                                POWER OF ATTORNEY

     KNOW ALL MEN BY THESE PRESENTS that each individual whose signature appears
below constitutes and appoints Richard D. Callahan and/or Marianne R. O'Connor
his true and lawful attorney-in-fact and agent with full power of substitution,
for him and his name, place and stead, in any and all capacities, to sign any
and all amendments to this Annual Report on Form 10-K, and to file the same,
with all exhibits thereto, and all documents in connection therewith, with the
Securities and Exchange Commission, granting unto said attorney-in-fact and
agent full power and authority to do and perform each and every act and thing
requisite and necessary to be done in and about the premises, as fully to all
intents and purposes as he might or could do in person, hereby ratifying and
confirming all that said attorney-in-fact and agent, or his substitute, may
lawfully do or cause to be done by virtue thereof.

     Pursuant to the requirements of the Securities Exchange Act of 1934, this
Annual Report on Form 10-K and Power of Attorney have been signed below by the
following persons in the capacities and on the dates indicated:

Name                                    Title                     Date
----                                    -----                     ----

     /s/Richard D. Callahan             President and Chief       March 16, 1999
-----------------------------           Executive Officer, 
Richard D. Callahan                     Director           
                                        


     /s/Joseph P. Ganey                 Chairman of the Board     March 16, 1999
-----------------------------
Joseph P. Ganey


     /s/Marianne R. O'Connor            Treasurer and Chief       March 16, 1999
-----------------------------           Financial Officer
Marianne R. O'Connor                               



                                       17
<PAGE>
 
                                        Director                  March __, 1999
-----------------------------
Brian D. Baird


     /s/John Bisgrove, Jr.              Director                  March 16, 1999
-----------------------------
John Bisgrove, Jr.


     /s/Peter J. Emerson                Director                  March 16, 1999
-----------------------------
Peter J. Emerson


     /s/Arthur A. Karpinski             Director                  March 16, 1999
-----------------------------
Arthur A. Karpinski


     /s/Henry D. Morehouse              Director                  March 16, 1999
-----------------------------
Henry D. Morehouse


     /s/Edward D. Peterson              Director                  March 16, 1999
-----------------------------
Edward D. Peterson


     /s/Lewis E. Springer, II           Director                  March 16, 1999
-----------------------------
Lewis E. Springer, II



                                       18
<PAGE>
 
                                  EXHIBIT INDEX


          Number                          Description
          ------                          -----------

          3(A)(I)   Restated Certificate of Incorporation of Registrant,
                    incorporated by reference to the Registrant's Registration
                    Statement on Form 8-A (No. 0-18301), filed with the
                    Commission on November 12, 1991, wherein such exhibit is
                    designated Exhibit 2(I)(2)(a).

          3(A)(II)  Certificate of Amendment of the Certificate of Incorporation
                    of Registrant, incorporated by references to the
                    Registrant's Quarterly Report on Form 10-Q for the quarter
                    ended September 30, 1996, filed with the Commission on
                    November 7, 1996, wherein such exhibit was designated
                    Exhibit 3.1.

          3(B)      Bylaws of Registrant, incorporated by reference to the
                    Registrant's Quarterly Report on Form 10-Q for the quarter
                    ended September 30, 1995, filed with the Commission on
                    November 13, 1995, wherein such exhibit is designated
                    Exhibit 3(ii).

                                   ***********

                    Compensatory Plans or Arrangements

          10(A)     Employment Agreement with Richard D. Callahan, incorporated
                    by reference to Registrant's Quarterly Report on Form 10-Q
                    for the quarter ended March 31, 1997, filed with the
                    Commission on May 14, 1997, wherein such exhibit is
                    designated 10(A).

          10(B)     Employment Agreement with Marianne R. O'Connor, incorporated
                    by reference to Registrant's Quarterly Report on Form 10-Q
                    for the quarter ended March 31, 1997, filed with the
                    Commission on May 14, 1997, wherein such exhibit is
                    designated 10(C).

          10(C)     Employment Agreement with Richard J. Notebaert, Jr.,
                    incorporated by reference to Registrant's Quarterly Report
                    on Form 10-Q for the quarter ended March 31, 1997, filed
                    with the Commission on May 14, 1997, wherein such exhibit is
                    designated 10(B).

          10(D)     Employment Agreement with Henry M. O'Reilly, incorporated by
                    reference to Registrant's Quarterly Report on Form 10-Q for
                    the quarter ended March 31, 1997, filed with the Commission
                    on May 14, 1997, wherein such exhibit is designated 10(D).



                                       19
<PAGE>
 
          10(E)     Employment Agreement with W. Anthony Shay, Jr., incorporated
                    by reference to Registrant's Quarterly Report on form 10-Q
                    for the quarter ended March 31, 1997, filed with the
                    Commission on May 14, 1997, wherein such exhibit is
                    designated Exhibit 10(D).

          10(F)     Amended and Restated 1988 Stock Option Plan, incorporated by
                    reference to Registrant's Registration Statement on Form S-8
                    (No. 33-94214), filed with the Commission on June 29, 1995,
                    wherein such exhibit is designated Exhibit 99.

          10(G)     1996 Stock Option Plan, incorporated by reference to
                    Registrant's Registration Statement on Form S-8
                    (No.333-10063), filed with the Commission on August 13,
                    1996, wherein such exhibit is designated Exhibit 99.

          10(H)     Stock Purchase Incentive Program, incorporated by reference
                    to Registrant's Annual Report on form 10-K for the fiscal
                    year ended December 31, 1996, filed with the Commission on
                    March 27, 1997, wherein such exhibit is designated Exhibit
                    10(I).

          10(I)     Description of Iroquois Bancorp, Inc. Annual Management
                    Incentive Plan.

          10(J)     Retirement Benefits Agreement with Richard D. Callahan,
                    incorporated by reference to Registrant's Annual Report on
                    Form 10-K for the fiscal year ended December 31, 1994, filed
                    with the Commission on March 29, 1995, wherein such exhibit
                    is designated 10(L).

          10(K)     Separation Agreement with James H. Paul, incorporated by
                    reference to Registrant's Quarterly Report on 10-Q for the
                    quarter ended March 31, 1997, filed with the Commission on
                    May 14, 1997, wherein such exhibit is designated Exhibit
                    10(F).

                                  ************

          13        Annual Report to Shareholders for Fiscal Year Ended December
                    31, 1998.

          21        List of Subsidiaries.

          23(A)     Consent of KPMG LLP with respect to the Annual Report on
                    Form 10-K for the Fiscal Year Ended December 31, 1998.


                                       20
<PAGE>
 
          23(B)     Consent of Fagliarone Group P.C. with respect to Exhibit 99
                    of the Annual Report on Form 10-K for the Fiscal Year Ended
                    December 31, 1998.

          24        Power of Attorney, included with the Signature Page of this
                    Annual Report on Form 10-K.

          99        Iroquois Bancorp, Inc. 401(k) Savings Plan Financial
                    Statements and Schedules for the Fiscal Years Ended December
                    31, 1998 and 1997, together with Independent Auditors'
                    Report Thereon of Fagliarone Group P.C. for the year ended
                    December 31, 1998 and KPMG LLP for the year ended December
                    31, 1997.



                                       21