Objective: To enhance evidence‐based knowledge on long‐term sequalae in patients with surgically corrected obstructing Müllerian anomalies. Methods: This long‐term case–control study included patients with menstrual outflow obstruction due to congenital anomalies of the uterus or vagina, who were at least 18 years old, and for whom 2 years had elapsed since the first surgery at the start of this study. The control group consisted of women without current gynecological problems. Patients underwent a surgical correction at the Radboud University Medical Center Nijmegen between 1980 and 2013. Of 78 patients approached, 38 (49%) were included in this study. The control group consisted of 54 females. The main outcome measures were pain and health state. The following questionnaires were used: Visual Analogue Scale pain scores, European Quality of Life–5 Dimensions questionnaire (EQ‐5D‐3L) and the adapted Endometriosis Health Profile questionnaire (EHP‐30). Results: Patients had higher actual and maximum abdominal pain scores compared with controls (11 vs 0 [P = 0.007] and 48 vs 21 [P = 0.035], respectively). Based on the EQ‐5D‐3L scores, patients had more pain and discomfort (P = 0.005), more mood problems (P = 0.023), and a poorer subjective health state (P = 0.002) and self‐rated health state (P = 0.031). Based on the EHP‐30, patients had a significant poorer self‐rated health state on four out of five subscales. Conclusion: In this study, following surgically corrected menstrual obstruction, patients had statistically significant higher abdominal pain scores and a poorer self‐rated health state compared with controls. Synopsis: Surgically corrected menstrual outflow obstructions lead to higher abdominal pain scores and a poorer self‐rated health state. Prompt and accurate diagnosis of menstrual outflow obstruction is of utmost importance. [ABSTRACT FROM AUTHOR]