When the disease involves the small bowel, it usually has a benign course, but in rare circumstances, it may present as abdominal emergency. Invasive bowel endometriosis can present as bowel obstruction. The major cause of obstruction is stricture formation and adhesions, which occasionally mimic Crohn's disease or a malignancy in its clinical presentation.

Gastrointestinal endometriosis is suggested by dysmenorrhea, menorrhagia or perimenstrual symptoms. Frank intestinal symptoms are usually associated with intestinal obstruction. While intestinal symptoms may occur during or be exacerbated by the menses, this association may not always be present. The symptoms coincide with menstruation in only 18-40% of the cases. A recurring crampy lower or mid-abdominal pain is the most common presenting symptom for both intestinal endometriosis and Crohn's disease. Other symptoms which may occur in both entities include diarrhea, constipation, nausea, vomiting, fever, anorexia, and weight loss.

A case report published on January 7, 2008 in the World Journal of Gastroenterology describes a desperate patient who presented to Dr. Zafer Teke of Pamukkale University Hospital, Turkey, in 2006. This patient was quite a challenge for Dr. Teke. She was 31 years old with perimenstrual lower and mid-abdominal pain irradiating to the back, and lower abdominal fullness for 3 years, at first monthly, but later continuous, and gradually increasing in severity. She gave a history of moderate dysmenorrhea and menorrhagia, but no dyspareunia. Her only medication was an oral contraceptive. She had delivered a healthy baby.