<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, 1999

[ ]    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 incorporation           (I.R.S. Employer
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. [X]
<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 29, 2000 was
$24,501,992 based upon the closing sale price of $14.75 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 29,
2000 was 2,306,880.


                       Documents Incorporated by Reference
                       -----------------------------------

Portions of the Registrant's Annual Report to Shareholders for the fiscal year
ended December 31, 1999 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 27, 2000 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 without limitation, 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.
<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.  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 7 through 24 of the Company's Annual Report to
Shareholders for the fiscal year ended December 31, 1999 (the "1999 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 Cayuga County population
declined by 1.3% or 1,049 people between 1990 and 1998.  Oneida County led the
state in population decline from 1990 to 1998 with 8.1%, or 20,208 people
leaving the county.  Oswego County showed a modest gain of 1.8% or 2,221 people.
The Syracuse MSA declined by 1.0%, or 7,597 people during the same period.

  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

                                       3
<PAGE>

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 1999, the Central New York economy slowed.  Total nonagricultural
employment in the Syracuse MSA increased just 0.6%, compared to a national
average of 2.4%.  Service sector jobs grew the most, adding 1,200.  Government
was second increasing by 800 jobs.  Manufacturing lost 200 jobs after good gains
in 1998.  Most other industry groupings showed little growth or small declines.

  The unemployment rate for the Syracuse MSA was 4.3% for December 1999 up from
3.6% a year earlier.  The unemployment rate for New York State for December 1999
was 4.5% while the national rate was 4.1%.  The December year over year
unemployment rate for Cayuga County increased from 5.2% in 1998 to 5.4% in 1999.
Oneida County remained at 3.8% while Oswego County increased from 5.6% to 6.9%
The unemployment rate for the Rochester MSA increased from 3.6% to 4.0%, and the
Utica MSA increased from 4.1% to 4.2%.

  The Central New York housing market remained strong during 1999.  Sales in the
Syracuse MSA were 15.5% higher than 1998 while the median sales price increased
8.1%.  Nationally, sales were up 5.9% with an increase in the median sales price
of 3.6%. The backlog of unsold homes continued to decline in the Company's
primary market areas.  The Rochester area housing market also remained strong
during 1999.  Home sales in most areas slowed with the rise in interest rates
through the fourth quarter of the year.

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.  It is expected that
competition will intensify with financial modernization, the redeployment of
technology dollars from Y2K concerns to new product and delivery technologies,
and investor expectations for growth.

  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.  As merger and acquisition activity has reduced the
number of bank competitors, community banks from contiguous areas are entering
the primary market areas of the subsidiaries with denovo branch banking offices.

                                       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
     1999 Annual Report to Shareholders in Management's Discussion and Analysis
     on page 9 in Table 1 - Net Interest Income Analysis, and on page 10 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 1999 Annual Report to Shareholders in Management's Discussion
     and Analysis on page 17 in Table 6 - Securities and on page 18 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 1999 Annual Report to Shareholders in Management's
          Discussion and Analysis on page 12 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 1999 Annual Report to Shareholders in Management's
          Discussion and Analysis on page 13 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 1999 Annual Report to Shareholders in
               Management's Discussion and Analysis on page 16 in Table 5 -
               Summary of Nonperforming 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 1999 Annual Report to Shareholders in
               Management's Discussion and Analysis on pages 16 and 17, in the
               discussion under the caption Nonperforming 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, 1999, 1998 and 1997, there were no foreign loans
               outstanding.

          4.   Loan Concentrations

               Information required by this section of Guide 3 is presented in
               the Registrant's 1999 Annual Report to Shareholders on page 44 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 1999 Annual Report to Shareholders in Management's
          Discussion and Analysis on page 15 in Table 4 - Allowance for Loan
          Losses, in the discussion on pages 14 to 16 under the caption
          Allowance for Loan Losses and in the discussion on pages 16 and 17
          under the caption Nonperforming 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 1999 Annual Report to Shareholders in Management's
          Discussion and Analysis on page 15 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 1999 Annual Report to Shareholders in Management's Discussion
     and Analysis on page 9 in Table 1 - Net Interest Income Analysis, on page
     19 in Table 8 - Deposits and on page 19 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 1999 Annual Report to Shareholders on page 6 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 1999 Annual Report to Shareholders on pages 37 and 38 in note
     (7) of the Notes to Consolidated Financial

                                       6
<PAGE>

     Statements 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, 1999 and 1998 and in the discussion therein under the caption
     Borrowings, which tabular information and discussions are incorporated
     herein by reference.


Employees

  At December 31, 1999, the Company and its Subsidiaries had 171 full-time and
30 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 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, 1999,
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 or 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.

  On November 12, 1999, the Gramm-Leach-Bliley Act, (the "GLB Act") of 1999 was
signed into law.  The GLB Act represents a sweeping reform of financial services
regulation and permits the creation of new financial services holding companies
that can offer a full range of financial products pursuant to regulatory reform
based on functional regulation financial services.  The legislation eliminates
the legal barrier to affiliations among banks and securities firms, insurance
companies, and other financial service companies and provides financial
organizations with flexibility in structuring these new affiliations while
preserving appropriate safeguards through regulation.

  Under the GLB Act, the Federal Reserve Board remains the primary supervisor
for holding companies and implements a system of functional regulation intended
to utilize the strengths of various federal and state regulators.  A key feature
of the GLB Act is the establishment of a minimum federal standard for financial
privacy pursuant to which all financial institutions must maintain a written
privacy policy that is disclosed to all customers at the time a customer
relationship is established and not less than annually to all customers of the
institution.  The GLB Act provides for regulation of bank securities activities,
eliminating the blanket exemption previously granted to banks from the
definition of "broker" and imposes, instead, limited exemptions to enable banks
to continue to perform some of the traditional bank securities activities
without registration as a broker.  The Act also amends federal securities laws
to include banks within the general definition of dealer and eliminates the
exclusion of banks from the definition of investment advisor.

  Because the legislation is so very new and the changes are radical, the
Company cannot yet determine how it will be affected by the GLB Act.  To date,
the Company's bank subsidiaries have adopted  a financial privacy policy for
disclosure to their customers and the Company is considering whether it would be
advantageous to implement any new products or services and whether any corporate
restructuring for financial services activities of its subsidiaries will be
appropriate.

                                       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 one office in Utica, one office in New Hartford, one office in
Waterville, and one office in Clinton, that are all owned and utilized as
banking offices by Homestead Savings. The Company is presently constructing a
banking office in Rome, New York for use by Homestead Savings. Until its
completion, the Company is also leasing banking office space in the Mohawk Acre
Shopping Plaza in Rome, New York. 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      57        President and Chief Executive Officer
Robert B. Bantle         48        Senior Vice President
Marianne R. O'Connor     45        Treasurer and Chief Financial Officer
W. Anthony Shay, Jr.     57        Vice President

</TABLE>

           All of the foregoing executive officers except Mr. Bantle were
elected by the Company's board of directors at its first board meeting in
January for the fiscal year. Mr. Bantle, who was hired in June 1999, was elected
by the Company's board of directors at its July meeting. 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>

  Robert B. Bantle, Senior Vice President, joined Cayuga Bank in June 1999.
From 1992 until that time, he was Senior Vice President - Community Banking for
First National Bank of Rochester. Prior to joining First National, he served for
three years with Central Trust Company of Rochester as Senior Vice President -
Human Resources & Quality and for fifteen years with Fleet Bank and its
predecessors in human resources, retail banking, and strategic planning.


  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.


  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 47 of the Company's 1999
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 6
of the Company's 1999 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 1999 Annual Report to Shareholders on pages 7 through 24 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 21 through 23 and to Table 10 - Net
Portfolio Value Analysis on page 22 and Table 11 - Interest Rate Sensitivity
Table on page 23 of Management's Discussion and Analysis in the Company's 1999
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 1999 Annual
Report to Shareholders on pages 26 through 46 thereof, along with the Unaudited
Summarized Quarterly Financial Information on page 47 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 27, 2000 (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 15 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 1999 Annual Report to Shareholders annexed
               hereto as Exhibit (13):

                    Report of Independent Auditors.

                    Consolidated Balance Sheets as of December 31, 1999 and
                    1998.

                    Consolidated Statements of Income for each of the years in
                    the three-year period ended December 31, 1999.

                    Consolidated Statements of Cash Flows for each of the years
                    in the three-year period ended December 31, 1999.

                    Consolidated Statements of Shareholders' Equity and
                    Comprehensive Income for each of the years in the three-year
                    period ended December 31, 1999.

                    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 Robert B. Bantle, incorporated by
                    reference to Registrant's Quarterly Report on Form 10-Q for
                    the quarter ended June 30, 1999, filed with the Commission
                    on August 12, 1999, wherein such exhibit is designated
                    10(L).

          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(E).

          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)     Amended & Restated 1996 Stock Option Plan, incorporated by
                    reference to Registrant's Amendment No. 1 to Registration
                    Statement on Form S-8 (No.333-10063), filed with the
                    Commission on February 2, 2000, 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, incorporated by reference to Registrant's
                    Annual Report on Form 10-K for the fiscal year ended
                    December 31, 1998, filed with the Commission on March 26,
                    1999, wherein such exhibit is designated Exhibit 10(I).

          10(J)     Incentive and Advance Agreement with Robert B. Bantle,
                    incorporated by reference to Registrant's Quarterly Report
                    on Form 10-Q for the quarter ended June 30, 1999, filed with
                    the Commission on August 12, 1999, wherein such exhibit is
                    designated 10(M).

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

          13        Annual Report to Shareholders for Fiscal Year Ended December
                    31, 1999.

          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, 1999.

          23(B)     Consent of The Fagliarone Group P.C. with respect to
                    Exhibit 99 of the Annual Report on Form 10-K for the fiscal
                    year ended December 31, 1999.

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

          27        Financial Data Schedule

          99        Iroquois Bancorp, Inc. 401(k) Savings Plan Financial
                    Statements and Schedules for the fiscal years ended December
                    31, 1999 and 1998, together with Independent Auditors'
                    Report Thereon of The Fagliarone Group P.C. for the years
                    ended December 31, 1999 and 1998.

                                       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 9, 2000.

                                     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:


<TABLE>
<CAPTION>
Name                                       Title                                  Date
----                                       -----                                  ----
<S>                                        <C>                                    <C>


      /s/Richard D. Callahan               President and Chief                    March 9, 2000
-----------------------------------        Executive Officer,
Richard D. Callahan                        Vice Chairman of the Board



      /s/Joseph P. Ganey                   Chairman of the Board                  March 10, 2000
-----------------------------------
Joseph P. Ganey



      /s/Marianne R. O'Connor              Treasurer and Chief                    March 9, 2000
-----------------------------------        Financial Officer
Marianne R. O'Connor


</TABLE>

                                       17
<PAGE>

<TABLE>
<S>                                        <C>                                    <C>

       /s/Brian D. Baird                      Director                               March 10, 2000
  ----------------------------------
  Brian D. Baird



       /s/John Bisgrove, Jr.                  Director                               March 10, 2000
  ---------------------------------
  John Bisgrove, Jr.



       /s/Peter J. Emerson                    Director                               March 10, 2000
  ---------------------------------
  Peter J. Emerson



       /s/Arthur A. Karpinski                Director                                March 10, 2000
  ---------------------------------
  Arthur A. Karpinski



       /s/Henry D. Morehouse                  Director                               March 10, 2000
  ---------------------------------
  Henry D. Morehouse



       /s/Edward D. Peterson                  Director                               March 10, 2000
  ---------------------------------
  Edward D. Peterson



       /s/Lewis E. Springer, II               Director                               March 10, 2000
  ---------------------------------
  Lewis E. Springer, II
</TABLE>

                                       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 reference 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 Robert B. Bantle, incorporated by
               reference to Registrant's Quarterly Report on Form 10-Q for the
               quarter ended June 30, 1999, filed with the Commission on August
               12, 1999, wherein such exhibit is designated 10(L).

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(E).

                                       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)          Amended and Restated 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, incorporated by reference to Registrant's Annual Report on
               Form 10-K for the fiscal year ended December 31, 1998, filed with
               the Commission on March 26, 1999, wherein such exhibit is
               designated Exhibit 10(I).

10(J)          Incentive and Advance Agreement with Robert B. Bantle,
               incorporated by reference to Registrant's Quarterly Report on
               Form 10-Q for the quarter ended June 30, 1999, filed with the
               Commission on August 12, 1999, wherein such exhibit is designated
               10(M).


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


13             Annual Report to Shareholders for Fiscal Year Ended December 31,
               1999.

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, 1999.

                                       20
<PAGE>

23(B)          Consent of The Fagliarone Group P.C. with respect to Exhibit
               99 of the Annual Report on Form 10-K for the Fiscal Year Ended
               December 31, 1999.

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

27             Financial Data Schedule

99             Iroquois Bancorp, Inc. 401(K) Savings Plan Financial Statements
               and Schedules for the Fiscal Years Ended December 31, 1999 and
               1998, together with Independent Auditors' Report Thereon of The
               Fagliarone Group P.C. for the years ended December 31, 1999 and
               1998.

                                       21