An imperforate hymen is a condition where the central portion of the epithelial membrane at the vaginal vestibule has failed to regress in the normal fashion. This layer creates a complete or almost complete barrier, obstructing the outflow of menstrual blood; this can result in hematocolpos and hematometra (hematometrocolpos, ie, accumulation of blood in the reproductive tract). There are multiple lesser variations of this, including microperforation of the hymen or the presence of a transverse or vertical septum / band.

Despite this being a congenital anomaly, presentation will usually take place around the expected time of menarche (13-15 years of age). Patients may present with cyclic abdominal, lower back, or pelvic pain, amenorrhea, constipation, or pain with urination or defecation. Some cases will be noted at birth due to a thin bulging membrane resulting from mucous buildup behind the hymen.

Patients with microperforation, transverse, or vertical septums will usually present somewhat later and often have complaints of inability to pass a tampon, malodorous discharge (due to partial outflow obstruction), or difficulty with penetrative intercourse.