As we strive to make science education more inclusive, more research is needed to fully understand gender gaps in academic performance and in-class participation in the life sciences. Studies suggest that male voices dominate introductory biology courses, but no studies have been done on upper-level courses. Results on achievement gender gaps in biology vary and often conflict, and no studies have been done on the correlation between participation and academic performance gaps. We observed 34 life sciences courses at all levels at a large private university. Overall, males were more likely to participate than their female peers, but these gender gaps varied from class to class. Females participated more in classes in which the instructor called on most hands that were raised or in classes with more females in attendance. Performance gender gaps also varied by classroom, but female final course grades were as much as 0.2 SD higher in classes with a female instructor and/or a female student majority. Gender gaps in participation and final course grades were positively correlated, but this could be solely because female students are more likely to both participate more and earn higher grades in classes with many females in attendance.