Background: Recent initiatives in cardiothoracic (CT) surgery education have been aimed at early tracking, emphasizing specialization during the final years of residency. This study was performed to examine the impact of subspecialization on graduate assessment of quality of training and to identify educational gaps. Methods: Surveys were sent to 119 surgeons who completed thoracic surgery residency at Washington University in St. Louis, Missouri between 1958 and 2017. Surveys evaluated transition-to-practice preparedness in patient care, technical skills, and qualifying and certifying examinations. A total of 78 surveys were returned complete, and 14 were returned “deceased” or “address unknown.” Clinical practices included combined CT surgery (n = 22; 28%) and subspecialty cardiac (n = 28; 36%) or thoracic surgery (n = 28; 36%). Responses were quantified on five-point Likert scales. Statistical analyses compared excellent (five points) with less than excellent (one to four points). Results: Graduates who practiced combined CT surgery were more likely to report excellent preparation for qualifying examinations (cardiac, 60.7% vs thoracic, 35.7% vs CT, 86.4%; p = 0.001) and certifying examinations (cardiac, 71.4% vs thoracic, 53.6% v. CT, 86.4%; p = 0.042). Compared with thoracic surgery and combined CT surgery graduates, graduates who practiced cardiac surgery were more likely to indicate excellent preparation for performing adult cardiac surgery (cardiac, 85.2% vs thoracic, 34.8% vs CT, 81.8%; p < 0.001), although they felt least prepared to perform general thoracic surgery (cardiac, 85.7% vs thoracic, 100.0% vs CT, 100.0%; p = 0.023). Conclusions: Graduates with combined CT surgery practices self-reported greater examination preparation and technical training compared with graduates who subspecialized in cardiac or thoracic surgery. Subspecialization led to perceived deficiencies among graduates in nonspecialty areas. This should be considered when developing new CT residency training paradigms.