A typical pelvic exam usually can't detect endometriosis unless there is a pelvic mass or lesion in the ovary causing a cyst, which is relatively rare. Laparoscopy also cannot detect all cases of the disease since some women have deep (endometriosis) disease, meaning the surface projection of the transplanted endometrium is tiny or invisible and the majority of the disease is imbedded deep into the tissue; other women have superficial disease, where the extent of the disease is readily seen by laparoscopy. Often, women have a combination of both types of lesions. Pain is usually greater in women with deep disease than superficial disease. A detailed medical history may offer the earliest clues to your health care professional that could lead to the correct diagnosis.

A laparoscope is commonly employed to diagnose endometriosis and may also be used to treat it. Performed under general anesthesia, laparoscopy allows a surgeon to view abnormalities in the pelvic region by inserting a miniature telescope through the abdominal wall, usually through the navel. A laparoscopy shows where adhesions or other abnormalities caused by endometriosis are located, their size and the extent of the problem.

If endometriostic lesions can be seen, this diagnosis is relatively straightforward. However, the disease is sometimes not easily visible. It can be hidden inside adhesions or underneath the lining of the abdominal cavity. Because the implants of endometriosis may not be visible by laparoscopy, some practitioners make the diagnosis based on clinical evaluation and response to medication.

Ultrasound, computed axial tomography (CAT) scans, and magnetic resonance imaging (MRI) — all ways of creating visual images of hard-to-view parts of the body, in this case, the pelvic area, are generally not considered effective ways to diagnose endometriosis.