BACKGROUND: No data exist to define the opportunity costs related to instruction in endoscopic procedures in Royal College of Physicians and Surgeons of Canada-accredited teaching centres. Academic and institutional administrators expect staff to achieve acceptable performance standards. There is a need to measure some of the effects of training activity in the establishment of such standards.OBJECTIVE: To measure the effect of resident training in colonoscopy on real procedure times and, as a secondary goal, to estimate procedural losses related to the process of training.METHODS: Real procedure times for ambulatory colonoscopy in a single academic, hospital-based endoscopy unit were documented. Times for certified endoscopy instructors functioning solo were compared with times for procedures involving trainees at several levels of colonoscopic experience. Procedural reductions associated with resident training were estimated based on the parameters derived from the results. The analysis was executed retrospectively using prospectively collected data.RESULTS: Resident training prolonged procedure times for ambulatory colonoscopy by 50%. The trainee effect was consistent, although variable in degree, among a variety of endoscopy instructors. Such increased procedure times have the potential to reduce case throughput and endoscopist remuneration.CONCLUSIONS: Resident training in colonoscopy in a Canadian certified training program has significant negative effects on case throughput and endoscopist billings. These factors should be considered in any assessment of performance in similar training environments.