Abstract Background Laparoscopic training has become an important part of surgical education. Laparoscopic Roux-en-Y gastric bypass (RYGB) is the most common bariatric procedure performed. Surgeons must be well trained prior to operating on a patient. Multimodality training is vital for bariatric surgery. E-learning with videos is a standard approach for training. The present study investigates whether scoring the operation videos with performance checklists improves learning effects and transfer to a simulated operation. Methods/design This is a monocentric, two-arm, randomized controlled trial. The trainees are medical students from the University of Heidelberg in their clinical years with no prior laparoscopic experience. After a laparoscopic basic virtual reality (VR) training, 80 students are randomized into one of two arms in a 1:1 ratio to the checklist group (group A) and control group without a checklist (group B). After all students are given an introduction of the training center, VR trainer and laparoscopic instruments, they start with E-learning while watching explanations and videos of RYGB. Only group A will perform ratings with a modified Bariatric Objective Structured Assessment of Technical Skill (BOSATS) scale checklist for all videos watched. Group B watches the same videos without rating. Both groups will then perform an RYGB in the VR trainer as a primary endpoint and small bowel suturing as an additional test in the box trainer for evaluation. Discussion This study aims to assess if E-learning and rating bariatric surgical videos with a modified BOSATS checklist will improve the learning curve for medical students in an RYGB VR performance. This study may help in future laparoscopic and bariatric training courses. Trial registration German Clinical Trials Register, DRKS00010493 . Registered on 20 May 2016.