Background: In the US, bioscience programs now often have more women than men who earn degrees at all levels. Despite this, evidence still exists for gender inequity in bioscience and medical fields. For example, women with careers in these fields tend to get paid less and leave these fields more. Here, we present research investigating grade penalties. Grade penalties describe the difference between a students' grade point average and grade in a particular course when a students' grade in a class is lower than their grade point average (GPA). For example, a student has a grade penalty of 1 in a course if their GPA is 3.0 (B) and they receive a 2.0 (C) in the course. We hypothesize that grade penalties in these STEM courses can affect students' STEM-related self-concept negatively with potentially long-term consequences, e.g., in students' career choices. We investigated grade penalties in science courses for undergraduate students studying biosciences. We propose a framework that posits that students who receive grade penalties in a course may view themselves as less capable in that domain and that gender differences in grade penalties may be a useful measure of gender inequity in the classroom. Results: In this study, we examined grade penalties of 2445 students majoring in biological science or closely related fields across many commonly taken courses, many of which were mandatory. We find that on average, students received grade penalties in the 12 most commonly taken science courses for biosciences students at our institution. We also find that women had more extreme grade penalties than men in seven of the 12 science classes we investigated. Conclusions: The pattern of grade penalties found in this study across a range of courses may result in long-term consequences for students' STEM self-concept. Furthermore, women's decisions to pursue STEM careers may be affected more by the grade penalty received in required science courses than men's at least partly, because their grade penalties are often larger. Finally, the grade penalty measure can be easily computed by institutions concerned with equity.