Endometriosis is defined as the presence of endometrial glands and stroma outside the endometrial cavity and uterine musculature. This ectopic endometrial implants are usually located in the pelvis, but can occur nearly anywhere in the body. Endometriosis also shares many similarities with autoimmune diseases such as rheumatoid arthritis, Leśniowski-Crohn’s disease, and psoriasis. We report a case of a 45-year-old female, diagnosed as Leśniowski-Crohn’s disease, verified as endometriosis after operative treatment, and discussed the difficulties in the differential diagnosis in this case.