Segmental rectum resections for indications other than endometriosis were reported to result in up to 40% sexual dysfunctions. We, therefore, evaluated sexual function after low bowel resection (n = 33) for deep endometriosis in comparison with conservative excision (n = 23). Sexual function was evaluated with the FSFI-19 (Female Sexuality Functioning Index) and EHP 30 (Endometriosis Health Profile). The pain was evaluated with visual analogue scales. Linear excision and bowel resections improved FSFI, EHP 30, and postoperative pain comparably. By univariate analysis, a decreased sexual function was strongly associated with pain both before (p < 0.0001) and after surgery (p = 0.0012), age (p = 0.05), and duration of surgery (p = 0.023). By multivariate analysis (proc logistic), the FSFI after surgery was predicted only by FSFI before or EHP after surgery. No differences were found between low bowel segmental resection and a more conservative excision. In conclusion, improving pain after surgery can explain the improvement in sexual function. A deleterious effect of a bowel resection on sexual function was not observed for endometriosis. Sexual function in women with endometriosis can be evaluated using a simplified questionnaire such as FSFI-6.