ABSTRACT Background Gender disparities are prevalent in medicine, but their impact on surgical training is not well studied. Objective To quantify gender disparities in trainee intraoperative experiences and explore the variables associated with ratings of surgical autonomy and performance. Methods From September 2015 to May 2019, attending surgeons and trainees from 71 programs assessed trainee autonomy on a 4-level Zwisch scale and performance on a 5-level modified Dreyfus scale after surgical procedures. Multivariable regression models were used to examine the association of trainee gender with autonomy and performance evaluations. Results A total of 3255 trainees and attending surgeons completed 94 619 evaluations. Attendings gave lower ratings of operative autonomy to female trainees than male trainees when controlling for training level, attending, and surgical procedure (effect size B = −0.0199, P = .008). There was no difference in ratings of autonomy at the beginning of training (P = .32); the gap emerged as trainees advanced in years (B = −0.0163, P = .020). The gender difference in autonomy was largest for the most complex cases (B = −0.0502, P = .002). However, there was no difference in attending ratings of surgical performance for female trainees compared to male trainees (B = −0.0124, P = .066). Female trainees rated themselves as having less autonomy and worse performance than males when controlling for training level, attending, procedure, case complexity, and attending ratings (autonomy B = −0.0669, P < .001; performance B = −0.0704, P < .001). Conclusions While there was no significant difference in ratings of operative performance, a small difference between ratings of operative autonomy for female and male surgical trainees was identified.