Research on the STEM educational pipeline has focused on degree attainment, finding that students who take STEM courses in high school are more likely to declare a STEM major later on (Gottfried & Bozick, Education Finance and Policy 11:177–202, 2016) and tend to perform better in college (Sadler & Tai, Science Education, 85(2). 2001). Similarly, early academic preparedness has been linked with degree attainment and persistence (Engberg & Wolniak, Teachers College Record 115:1–27, 2013). However, completing the degree does not necessarily result in the same level of preparedness for graduate school or professional work. We investigate STEM students' course-taking behaviors using a large multi-cohort, multi-institution dataset. We find that even among students who earn the same STEM degree from the same schools, Black and Latinx students are less likely to have taken advanced courses and earn lower grades as well. Differences in how advanced courses are taken by racial and ethnic subgroups also persisted when only looking at courses the most central to students' own majors. These college STEM graduates represent the pool that might pursue graduate school and professional work. Our results indicate that students who attain their STEM degree may not be all equally educated and the pipeline of students prepared for graduate school may be even narrower than simple counts of how many students earn a degree suggests. Earlier academic background and preparedness in high school, particularly in quantitative reasoning, explains most of the course-taking differences even when controlling for socioeconomic status. We suggest that colleges may want to investigate the causes of these course-taking differences and intervene. [ABSTRACT FROM AUTHOR]