BACKGROUND: There are no studies reporting the rate of surgical site infection (SSI) after surgery for endometriosis, although this information is valuable when discussing the most appropriate treatment strategy with the patient. METHODS: We conducted a prospective cohort study in a university hospital and regional reference center for endometriosis. We sought to measure the rate of SSI after endometriosis surgery using prospective SSI post-discharge surveillance data and the hospital information system via an ad hoc algorithm using both diagnosis and procedure code classifications. RESULTS: Among 896 consecutive endometriosis surgical procedures, we identified 365 procedures with involvement of the gastrointestinal tract, defined as the deep invasive procedure (DIP) group, 107 procedures with involvement of an ovary, and 424 other procedures. Twelve SSI (all organ/space infections) were observed, all in the DIP group, corresponding to an overall SSI incidence of 1.3% 95% confidence interval (CI) 0.7-2.3, and an SSI incidence in the DIP group of 2.8%, 95% CI 1.5-4.9. The median delay between the procedure and the SSI was 6.5 days (range, 3-23). At least one micro-organism was found in 10 patients (four Escherichia coli, four Enterobacter cloacae, three Enteroccus faecalis, two Bacteroides fragilis, one Pseudomonas aeruginosa, one Candida albicans). CONCLUSION: A low overall rate of SSI after surgery for endometriosis was observed. Nevertheless, procedures with involvement of the intestinal tract were at risk of SSI.