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Endometriosis is commonly misdiagnosed, even among many experienced gynecologists. Gastrointestinal and genitourinary endometriosis is particularly difficult to diagnose, and is commonly mistaken for other pathologies, such as irritable bowel syndrome, interstitial cystitis, and even psychological disturbances. This leads to delays in diagnosis, mismanagement, and unnecessary testing. In this review, we will discuss the diagnosis and management of genitourinary and gastrointestinal endometriosis. Medical management may be tried first, but often fails in cases of urinary tract endometriosis. This is particularly important in cases of ureteral endometriosis because silent obstruction can lead to eventual kidney failure. Thus, we recommend complete surgical treatment in these cases. Bladder endometriosis may be managed more conservatively, and only if symptomatic, because these rarely lead to significant morbidity. In cases of bowel endometriosis, we recommend medical management first in all cases, and the least invasive surgical management only if medical treatment fails. This is due to the extensive nervous and vasculature supply to the lower rectum. Injury to these nerves and vessels can cause significant complications and postoperative morbidity.

Diagnostic and treatment guidelines for gastrointestinal and genitourinary endometriosis