Since the residency training program in internal medicine changed from a four-year to a three-year program in 2017 in Korea, issues of an optimal training program for the gastrointestinal (GI) fellowship has arisen. Currently, the evaluation criteria for a GI fellowship in Korea include the following; 1) the total number of assigned patients during the training period, 2) the number of GI endoscopy procedures, 3) attendance at academic conferences, and 4) research presentations. However, competency-based training should be introduced in the GI fellowship training program. The current issues of GI fellowship training in Korea include the following; 1) reorganization of the GI fellowship education system and consideration of an optimal training period following the introduction of the three-year internal medicine residency training program, 2) development of a standardized, competency-based GI fellowship training program, 3) provision of a support program for instructors in GI fellowship education, 4) introduction of a mentor-mentee system, 5) introduction of an accreditation system for GI fellowship, 6) supplementation of a GI sub-specialty qualification system, and 7) provision of benefits to GI sub-specialists.