Over 50,000 Ph.D. degrees in Science and Engineering (S&E) are awarded annually by United States (U.S.) universities, but few studies have systematically considered how the various aspects of doctoral training can influence the occupational outcomes of S&E doctoral graduates. This inquiry draws from the National Science Foundation's Scientists and Engineers Statistical Data System to investigate how the characteristics of U.S. degree-granting departments and institutions are associated with doctoral graduates' entrance into different career sectors (i.e., academia, industry, government). The conceptual framework is based on the Scientific and Technical Human Capital theory (Bozeman et al. in Int J Technol Manag 22(7-8):716-740, 2001) as well as Berger and Milem's (Higher Education: Handbook of Theory and Research, Agathon Press, New York, 2000) model of college impact. We find that a number of university and department factors are associated with the career choice of S&E doctoral graduates after finishing their Ph.D including: (a) structural characteristics, such as geographic location and faculty composition, (b) organizational behaviors, such as those symbolizing a program's relative emphasis on traditional academic work versus activities valued in industry, and (c) peer group characteristics such as a department's proportion of female and minority Ph.D. students. These results will be particularly informative for policy makers, faculty and administrators in S&E programs, and prospective doctoral students.