Background: Despite an increasing number of women in the field of surgery, bias regarding cognitive or technical ability may continue to affect the experience of female trainees differently than their male counterparts. This study examines the differences in the degree of operative autonomy given to female compared with male general surgery trainees. Methods: A smartphone app was used to collect evaluations of operative autonomy measured using the 4-point Zwisch scale, which describes defined steps in the progression from novice (“show and tell”) to autonomous surgeon (“supervision only”). Differences in autonomy between male and female residents were compared using hierarchical logistic regression analysis. Results: A total of 412 residents and 524 faculty from 14 general surgery training programs evaluated 8,900 cases over a 9-month period. Female residents received less autonomy from faculty than did male residents overall (P <.001). Resident level of training and case complexity were the strongest predictors of autonomy. Even after controlling for potential confounding factors, including level of training, intrinsic procedural difficulty, patient-related case complexity, faculty sex, and training program environment, female residents still received less operative autonomy than their male counterparts. The greatest discrepancy was in the fourth year of training. Conclusion: There is a sex-based difference in the autonomy granted to general surgery trainees. This gender gap may affect female residents’ experience in training and possibly their preparation for practice. Strategies need to be developed to help faculty and residents work together to overcome this gender gap.