STUDY QUESTION: To what extent are endometriosis and its related physical and mental symptoms associated with the perceived level of sexual functioning in women and their male partners? SUMMARY ANSWER: Dyspareunia and depressive symptoms are associated with impaired sexual functioning in women with endometriosis, whereas sexual functioning in their male partners is not affected. WHAT IS KNOWN ALREADY: Women with endometriosis suffer from more dyspareunia, lower sexual functioning, and lower quality of life. In qualitative studies, partners of women with endometriosis report that endometriosis affected their quality of life and produced relational distress. STUDY DESIGN SIZE, DURATION: In this cross-sectional study, sexual functioning in women with endometriosis (n = 83) and their partners (n = 74) was compared with sexual functioning in a control group of women attending the outpatient department for issues related to contraception (n = 40), and their partners (n = 26). PARTICIPANTS/MATERIALS, SETTING, METHODS: Women and partners were recruited in the Maastricht University Medical Centre (MUMC) and the VieCuri Medical Centre Venlo between June 2011 and December 2012. All participants were asked to complete a set of online questionnaires. MAIN RESULTS AND THE ROLE OF CHANCE: Response rates were 59.3% (83/140) for women with endometriosis and 52.3% (74/140) for their partners. Response rates in the control group were respectively 43.2% and 27.4% (41/95 and 27/95), of whom 40 women and 26 partners could be included in the study. Women with endometriosis as compared with the control group, reported significantly more frequent pain during intercourse (53% versus 15%, P < 0.001); higher levels of chronic pain (median VAS 2.0 cm versus 0.0 cm, P < 0.001); more impairment of sexual functioning (median Female Sexual Function Index 25.4 versus 30.6, P < 0.001); more impairment of quality of life (median Short Form-12 66.3 versus 87.2, P < 0.001); more pain catastrophizing (mean Pain Catastrophizing Scale 17.8 versus 8.5, P < 0.001), more depression and anxiety symptoms (median Hospital Anxiety and Depression Scale for depression 7 versus 4, P < 0.001 and for anxiety 4 versus 1, P < 0.001). Sexual functioning was comparable between male partners of women with endometriosis and male partners of the control group based on the International Index of Erectile Function. Logistic regression analyses showed that dyspareunia (OR 0.54; 95% CI 0.39–0.75) and depressive symptoms (OR 0.761; 95% CI 0.58–0.99) were independent and significant negative predictors for sexual functioning. Chronic pelvic pain (OR 0.53; 95% CI 0.35–0.81) and depressive symptoms (OR 0.65; 95% CI 0.44–0.96) were independent and significant negative predictors for quality of life. LIMITATIONS, REASONS FOR CAUTION: Patient recruitment was performed in one tertiary care centre and to a lesser extent one general hospital, possibly leading to an over-representation of patients with more severe endometriosis. All participating women had a partner and are therefore ‘survivors’ in relationship terms. This may have led to an underestimation of the impact of endometriosis on sexual functioning. WIDER IMPLICATIONS OF THE FINDINGS: It would be worthwhile to further explore the role of depressive symptoms in women with symptomatic endometriosis and to assess the effect of treatment of depressive symptoms on sexual functioning and quality of life. The fact that the partners did not report impaired sexual functioning could be a reassuring thought to women that might be discussed in the consulting room.