Background Resident perceptions of 2-year (2Y) vs 3-year (3Y) programs have never been characterized. The objective was to use the mandatory Thoracic Surgery Residents Association and Thoracic Surgery Directors Association In-Training Examination survey to compare perceptions of residents graduating from 2Y vs 3Y cardiothoracic programs. Methods Each year Accreditation Council for Graduate Medical Education cardiothoracic residents are required to take a 30-question survey designed by the Thoracic Surgery Residents Association and the Thoracic Surgery Directors Association accompanying the In-Training Examination with a 100% response rate. The 2013 and 2014 survey responses of residents graduating from 2Y vs 3Y training programs were compared. The Wilcoxon signed rank test was used to analyze ordinal and interval data. Results Graduating residents completed 167 surveys, including 96 from 2Y (56%) and 71 from 3Y (43%) programs. There was no difference in the perception of being prepared for the American Board of Thoracic Surgery examinations or amount of debt between 2Y and 3Y respondents. There was no difference in intended academic vs private practice. Graduating 3Y residents felt more prepared to meet case requirements and better trained, were more likely to pass their written American Board of Thoracic Surgery examinations, and were less likely to pursue additional training beyond their cardiothoracic residency. Conclusions There was no difference in field of interest, practice type, and amount of debt between graduating 2Y vs 3Y residents. Respondents from 2Y programs expressed more difficulty in meeting case requirements, whereas residents from 3Y programs felt more prepared for independent practice and had higher American Board of Thoracic Surgery written pass rates.