Endometriosis is a benign, estrogen-dependent gynecological condition characterized by presence of endometrial tissue outside the uterus. Endometriosis affects approximately 5–10% of women of reproductive age group and symptoms include chronic pelvic pain, dysmenorrhea, dyspareunia, and/or infertility. Endometrioma is a distinct presentation of endometriosis and may manifest in isolation or in association with other features of endometriosis and its association with infertility or reduced ovarian reserve remains controversial. This chapter covers the pathogenesis, effects of ovarian endometriosis on fertility, diagnosis of endometrioma, and treatment of infertile women with endometrioma. The ultimate goal of treatment in these patients is to achieve pregnancy, either spontaneously or using IVF.