The graduate medical education system is tasked with training competent and autonomous health care providers while also improving patient safety, delivering more efficient care, and cutting costs. Concerns about resident autonomy and preparation for independent and safe practice appear to be growing, and the field of surgery faces unique challenges in preparing graduates for independent practice. Multiple factors are contributing to an erosion of resident autonomy and decreased operative experience, including differing views of autonomy, financial forces, duty hours regulations, and diverse community health care needs. Identifying these barriers and developing solutions to overcome them are vital first steps in reversing the trend of diminishing autonomy in surgical residency training. This Commentary highlights the problem of decreasing autonomy, outlines specific threats to resident autonomy, and discusses potential solutions to mitigate their impact on the successful transition to independent practice.