Müllerian abnormalities may present with a wide range of symptoms including cyclic pelvic pain, dyspareunia, amenorrhea, pelvic mass, infertility, and recurrent pregnancy loss. Obstructive abnormalities are more likely to be associated with pelvic pain and endometriosis. Diagnosing an obstructive müllerian abnormality can be difficult and may require a combination of history, examination (potentially examination under anesthesia), radiologic imaging (ultrasound and/or MRI), laparoscopy, and hysteroscopy. Depending on the type of abnormality and the level of obstruction, patients may experience hematosalpinx (fallopian tube), hematometra (uterus), or hematocolpos (vagina).

Patients with imperforate hymen may present with primary amenorrhea, cyclic pelvic pain, and bulging hymenal tissue. Surgical repair includes removing the hymenal tissue and attaching the vaginal mucosa to the hymenal ring.

Patients with transverse vaginal may present in a similar manner to patients with imperforate hymen. However, a transverse vaginal septum can be associated with uterine malformations while hymenal abnormalities are not, and repair of the transverse vaginal septum is a more complex procedure involving resection of the septum and reanastomosis of the upper and lower segments of the vaginal mucosa. Vaginal atresia requires surgical correction involving creating a vaginal opening at the apex where hematometra can drain, and creating a new vagina with either the use of vaginal dilators or split-thickness skin grafts.

Two uterine abnormalities associated with outflow tract obstruction can present with pelvic pain; bicornuate uterus with a non-communicating rudimentary horn and uterine didelphys with obstructed Heim vagina and ipsilateral renal agenesis. The former is treated with laparoscopic resection of the noncommunicating horn; the latter is treated with resection of the wall of the obstructed vagina so both uteri can drain through the patent vagina.