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NIH Loan Repayment Program:
http://www.lrp.nih.gov

NIH Pathway to Independence Award (PA-07-297):
http://grants2.nih.gov/grants/new_investigators/QsandAs.htm

NIH Small Grant Program (RO3):
http://grants.nih.gov/grants/funding/r03.htm

USDA National Research Initiative Competitive Grants Program
http://www.csrees.usda.gov/funding/rfas/nri_rfa.html

US Department of Energy Office of Nuclear Physics Outstanding Junior Investigator Program:
http://www.science.doe.gov/grants/FAPN06-22.html

NSF Faculty Early Career Development (CAREER) Program:
http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=5262

NSF Research Initiation Grants and Career Advancement Awards to Broaden Participation in Biology (RIG CAA BP):
http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=10676

American Chemical Society – Arthur C. Cope Young Scholar Awards: http://www.chemistry.org/portal/a/c/s/1/acsdisplay.html?DOC=awards%5Cyngcopescholar.html

American Mathematical Society - Centennial Fellowships:
http://www.ams.org/employment/centflyer.html

William T. Grant Scholars Program:
http://www.wtgrantfoundation.org/info-url_nocat3042/info-url_nocat_show.htm?doc_id=76878&attrib_id=4398

Packard Fellowships for Science and Engineering:
http://www.packard.org/itemDetails.aspx?RootCatID=3&CategoryID=168

Many more listed here:

List of new investigator/young faculty grant programs:
http://www.spo.berkeley.edu/Fund/newfaculty.html