Abstract Background Colonoscopy exposes endoscopists to awkward postures and prolonged forces, which increases their risk of musculoskeletal injury. Patient positioning has a significant impact on the ergonomics of colonoscopy. Recent trials have found the right lateral decubitus position is associated with quicker insertion, higher adenoma detection rates, and greater patient comfort compared to the left lateral decubitus position. However, this patient position is perceived as more strenuous by endoscopists. Methods Nineteen endoscopists were observed performing colonoscopies during a series of four-hour endoscopy clinics. Durations of each patient position (right lateral decubitus, left lateral decubitus, prone, and supine) were recorded for all observed procedures (n = 64). Endoscopist injury risk was estimated by a trained researcher for the first and last colonoscopies of the shifts (n = 34) using Rapid Upper Limb Assessment (RULA), an observational ergonomic tool that estimates risk of musculoskeletal injury by scoring postures of the upper body and factors such as muscle use, force, and load. The total RULA scores were compared with a Wilcoxon Signed-Rank test for patient position (right and left lateral decubitus) and time (first and last procedures) with significance taken at p