Millennium Challenge Accountability Act of 2004 - Amends the Consolidated Appropriations Act, 2004 to: (1) direct the Comptroller General to conduct annual audits, evaluations, and investigations of the Millennium Challenge Corporation; (2) establish the Millennium Challenge Advisory Council; and (3) transfer statutory authority to the Foreign Assistance Act of 1961 for the Millennium Challenge program, the HELP Commission Act, and the Foreign Aid Impact Assessment Act.
Amends the Foreign Assistance Act of 1961 to repeal specified provisions respecting: (1) general development assistance; (2) prototype desalting plants; and (3) international disaster assistance.