Background and study aims The repair costs of gastrointestinal endoscopes account for a significant proportion of the total budget of an endoscopy unit. This study evaluated the repair costs of small-caliber endoscopes and conventional endoscopes used in esophagogastroduodenoscopy (EGD). Patients and methods A retrospective analysis of upper gastrointestinal endoscope damage and repair costs between April 2012 and May 2019 was performed at the Toyoshima Endoscopy Clinic. Conventional endoscopes (GIF-H260, GIF-HQ290, and GIF-H290Z) were used for transoral EGD while small-caliber endoscopes (GIF-XP260N and GIF-XP290N) were used for transnasal or transoral EGD. Results Three small-caliber endoscopes and five conventional endoscopes were used for 1,031 procedures and 31,192 procedures, respectively. The number of procedures/damage incidence for small-caliber endoscope and conventional endoscopes was 344 and 1950, respectively. Damage incidence for small-caliber endoscopes was significantly higher than for conventional endoscopes ( P = 0.014). Repair costs/procedure were $ 5.95 ± $132 for small-caliber endoscopes and $2.41 ± $115 for conventional endoscopes. Repair costs/procedure for small-caliber endoscopes were more than twice those for conventional endoscopes. Conclusions Small-caliber endoscopes are more fragile than conventional endoscopes.