Abstract Introduction Endometriosis is a benign condition that causes pain and infertility. Sexual dysfunction, particularly deep dyspareunia, is common in patients with endometriosis and interferes with quality of life and conjugal satisfaction. Aim The study aims to assess sexual function in women with deep infiltrating endometriosis. Method Fifty-seven women diagnosed with deep infiltrating endometriosis were recruited from Hospital Universitário Pedro Ernesto (HUPE) between July and December 2011. The control group comprised 38 healthy women recruited at the HUPE family planning clinic. Main Outcome Measures The main outcomes are full-scale and individual domain scores on the Female Sexual Function Index (FSFI), a validated questionnaire for functional assessment of sexual function in women. Results Patients with endometriosis had more pain in intercourse than controls, which correlates with lower scores in the FSFI pain domain. However, there were no statistically significant between-group differences in overall (full-scale) FSFI scores. Conclusion Women with endometriosis exhibit significant dysfunction in the pain domain of the FSFI questionnaire, but this finding was not sufficient to affect the overall sexual function.