Clinical performance evaluations are major components of medical school clerkship grades. But are they sufficiently objective? This study aimed to determine whether student and evaluator gender is associated with assessment of overall clinical performance. This was a retrospective analysis of 4,272 core clerkship clinical performance evaluations by 829 evaluators of 155 third-year students, within the Alpert Medical School grading database for the 2013-2014 academic year. Overall clinical performance, assessed on a three-point scale (meets expectations, above expectations, exceptional), was extracted from each evaluation, as well as evaluator gender, age, training level, department, student gender and age, and length of observation time. Hierarchical ordinal regression modeling was conducted to account for clustering of evaluations. Female students were more likely to receive a better grade than males (adjusted odds ratio [AOR] 1.30, 95% confidence interval [CI] 1.13-1.50), and female evaluators awarded lower grades than males (AOR 0.72, 95% CI 0.55-0.93), adjusting for department, observation time, and student and evaluator age. The interaction between student and evaluator gender was significant (P = .03), with female evaluators assigning higher grades to female students, while male evaluators' grading did not differ by student gender. Students who spent a short time with evaluators were also more likely to get a lower grade. A one-year examination of all third-year clerkship clinical performance evaluations at a single institution revealed that male and female evaluators rated male and female students differently, even when accounting for other measured variables.