Since the introduction of minimally invasive surgery, surgeons appear to be experiencing more occupational musculoskeletal injuries. The aim of this study is to investigate the current frequency and effects of occupational musculoskeletal injuries on work absence. An online questionnaire was conducted among all surgeons affiliated to the Dutch Society for Endoscopic Surgery, Gastrointestinal Surgery, and Surgical Oncology. In addition, this survey was conducted among surgeons, gynaecologists, and urologists of one cluster of training hospitals in the Netherlands. There were 127 respondents. Fifty-six surgeons currently suffer from musculoskeletal complaints, and 30 have previously suffered from musculoskeletal complaints with no current complaints. Frequently reported localizations were the neck (39.5 %), the erector spinae muscle (34.9 %), and the right deltoid muscle (18.6 %). Most of the musculoskeletal complaints were present while operating (41.8 %). Currently, 37.5 % uses medication and/or therapy to reduce complaints. Of surgeons with past complaints, 26.7 % required work leave and 40.0 % made intraoperative adjustments. More surgeons with a medical history of musculoskeletal complaints have current complaints (OR 6.1, 95 % CI 1.9-19.6). There were no significant differences between surgeons of different operating techniques in localizations and frequency of complaints, or work leave. Despite previous various ergonomic recommendations in the operating room, the current study demonstrated that musculoskeletal complaints and subsequent work absence are still present among surgeons, especially among surgeons with a positive medical history for musculoskeletal complaints. Even sick leave was necessary to fully recover. There were no significant differences in reported complaints between surgeons of different operating techniques. Almost half of the respondents with complaints made intraoperative ergonomic adjustments to prevent future complaints. The latter would be interesting for future research.