<Page>

                                                              Exhibit 99.906CERT

CERTIFICATION PURSUANT TO RULE 30a-2(b) UNDER THE INVESTMENT COMPANY ACT OF 1940

This certification is provided pursuant to Rule 30a-2(b) under the Investment
Company Act of 1940, and accompanies the report on Form N-CSR furnished to the
Securities and Exchange Commission on the date hereof of the JPMorgan U.S. Small
Company Opportunities Fund (the "Fund"), a series of J.P. Morgan Funds.

I, George C.W. Gatch, certify that:

1.   The Form N-CSR fully complies with the requirements of Section 13(a) or
     15(d) of the Securities Exchange Act of 1934, as applicable; and

2.   The information contained in the Form N-CSR fairly presents, in all
     material respects, the financial condition and results of the operations of
     the Fund.

/s/ George C.W. Gatch
- ----------------------
George C.W. Gatch
President

March 9, 2005
- ----------------------
Date


This certificate is furnished pursuant to the requirements of Form N-CSR and
shall not be deemed "filed" for purposes of Section 18 of the Securities
Exchange Act of 1934, or otherwise subject to the liability of that section, and
shall not be deemed to be incorporated by reference into any filing under the
Securities Act of 1933 or the Securities Exchange Act of 1934.

<Page>

CERTIFICATION PURSUANT TO RULE 30a-2(b) UNDER THE INVESTMENT COMPANY ACT OF 1940

This certification is provided pursuant to Rule 30a-2(b) under the Investment
Company Act of 1940, and accompanies the report on Form N-CSR furnished to the
Securities and Exchange Commission on the date hereof of the JPMorgan U.S. Small
Company Opportunities Fund (the "Fund"), a series of J.P. Morgan Funds.

I, Stephanie J. Dorsey, certify that:

1.   The Form N-CSR fully complies with the requirements of Section 13(a) or
     15(d) of the Securities Exchange Act of 1934, as applicable; and

2.   The information contained in the Form N-CSR fairly presents, in all
     material respects, the financial condition and results of the operations of
     the Fund.

/s/ Stephanie J. Dorsey
- -----------------------
Stephanie J. Dorsey
Treasurer

March 9, 2005
- ----------------------
Date


This certificate is furnished pursuant to the requirements of Form N-CSR and
shall not be deemed "filed" for purposes of Section 18 of the Securities
Exchange Act of 1934, or otherwise subject to the liability of that section, and
shall not be deemed to be incorporated by reference into any filing under the
Securities Act of 1933 or the Securities Exchange Act of 1934.