Currently, the U.S. population is undergoing major racial and ethnic demographic shifts that could affect the pool of individuals interested in pursuing a career in biomedical research. To achieve its mission of improving health, the National Institutes of Health must recruit and train outstanding individuals for the biomedical workforce. In this study, we examined the educational transition rates in the biomedical sciences by gender, race, and ethnicity, from high school to academic career outcomes. Using a number of educational databases, we investigated gender and racial/ethnic representation at typical educational and career milestones en route to faculty careers in biomedicine. We then employed multivariate regression methods to examine faculty career outcomes, using the National Science Foundation’s Survey of Doctorate Recipients. We find that while transitions between milestones are distinctive by gender and race/ethnicity, the transitions between high school and college and between college and graduate school are critical points at which underrepresented minorities are lost from the biomedical pipeline, suggesting some specific targets for policy intervention.