Each year the President submits a budget to Congress for funding the federal government for the next fiscal year. The Appropriations Committees in both the House and Senate use this budget as a guide in formulating the 10 separate appropriations bills that fund the entire federal government. The House and Senate each draft and pass separate appropriations bills that are debated and amended in a conference between the House and Senate and passed again in each chamber as one bill sent to the President to sign. The Congress is supposed to pass all 10 appropriations bills by October 1 – the beginning of the fiscal year.
The Federal government funds medical research in a variety of ways. The National Institutes of Health funds the majority of federally supported medical research. Congress appropriates funds for the NIH each year in the Labor, HHS Appropriations bill, allocating specific amounts of money to NIH and its various institutes. NIH is responsible for allocating that funding for specific medical research through competitive grants. Congress does not target or "earmark" funds within NIH for specific disease research.
The Federal government also funds medical research in a number of other agencies, such as the Department of Defense, the Department of Energy, and the Department of Education. Unlike the case for NIH, Congress can target funding toward a specific disease under these agencies.