Purpose: To determine whether prematriculation characteristics and career-setting preferences of MD-PhD graduates differ according to their schools′ funding from the National Institute of General Medical Sciences′ Medical Scientist Training Program (MSTP). Method: The Association of American Medical Colleges provided deidentified records for the national cohort of all 1993-2000 U.S. medical school matriculants, 3,180 of whom graduated with dual MD-PhD degrees by March 2, 2009. The authors examined prematriculation characteristics, educational outcomes, and career-setting preferences at graduation in association with MD-PhD program graduation from schools with long-standing MSTP-funded, recent MSTP-funded, and non-MSTP-funded programs. Results: Of 3,142 MD-PhD graduates with prematriculation data, 30% were women and 36% were nonwhite. Graduates from long-standing MSTP-funded schools (63% of 3,142 graduates) composed a more highly selective group academically (based on Medical College Admission Test scores) than did graduates from recent MSTP-funded (6%) and non-MSTP-funded schools (31%). Women and nonwhite graduates were more likely to have graduated from long-standing MSTP-funded schools. Controlling for MSTP funding and other variables, graduates with total debt of $100,000 or more were more likely to indicate non-research-related career-setting preferences (nonuniversity clinical practice: odds ratio [OR] 3.58, 95% confidence interval [CI] 1.86-6.87; undecided/other: OR 2.15, 95% CI 1.29-3.60). Neither gender nor race/ethnicity was independently associated with graduates′ career-setting preferences. Conclusions: Women and nonwhite MD-PhD graduates more likely graduated from long-standing MSTP than non-MSTP-funded schools. Controlling for institutional MSTP funding, MD-PhD graduates with high debt were more likely to indicate non-research-related career-setting preferences.