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The cause of endometriosis is unknown. One theory is that the endometrial tissue is deposited in unusual locations by the retrograde flow of menstrual debris through the Fallopian tubes into the pelvic and abdominal cavities. The cause of this retrograde menstruation is not clearly understood. It is clear that retrograde menstruation is not the only cause of endometriosis, as many women who have retrograde menstruation do not develop the condition.
Another possibility is that areas lining the pelvic organs possess primitive cells that are able to develop into other forms of tissue, such as endometrium. (This process is termed coelomic metaplasia.)
It is also likely the direct transfer of endometrial tissues at the time of surgery may be responsible for the endometriosis implants occasionally found in surgical scars (for example, episiotomy or Cesarean section scars). Transfer of endometrial cells via the bloodstream or lymphatic system is the most plausible explanation for the rare cases of endometriosis that are found in the brain and other organs remote from the pelvis.
Finally, there is evidence that some women with endometriosis have an altered immune response in women with endometriosis, which may affect the body’s natural ability to recognize ectopic endometrial tissue.
Source : Medicine.net