The mechanisms involved in the development of the disease are not completely understood: it is possible that some fragments of uterine lining are not removed during menstruation. Snippets move forward through the fallopian tubes and are fixed on other organs of the pelvic cavity (ovaries, bladder, rectum, colon), sometimes reaching up to the lungs. This attachment takes the form of cysts, most commonly located on the muscles of the uterus: in this case is called the adenomyosis disease.

Endometrium is under hormonal fluctuations during the menstrual cycle. Similarly, the fragments that have migrated to other parts of the body will react to the hormonal changes. Endometrium is sensitive to the action of estrogen and progesterone, and the decreased level of these hormones in the blood will result in the bleeding that characterizes menstruation. Fragments of endometrium will react in a similar fashion and will bleed during menstruation, just like the uterine lining.

On the other hand, endometriosis appears to be the consequence of a trauma of the cervix, following a biopsy, an electrocoagulation, a laser surgery or after a conization (ablation of the cervix as part of the con).
Pain can be explained by the fact that in the abdominal cavity organs are in contact with each other, separated by a fine membrane, on which fragments of endometrium may attach. During disease evolution, areas affected by endometriosis scars and give birth to grip. Depending on the organs between which these bonds appear, the location of the pain is variable. In the ovaries, endometriosis leads to pain that can be explained by compression and eventually by breaking hemorrhagic cysts.