Ovarian endometriomas are a common and specific manifestation of the disease endometriosis. In vitro fertilization (IVF) treatment in the words of the European Society of Human Reproduction and Embryology (ESHRE) Special Interest Group (SIG) on Endometriosis appears to be appropriate in patients with advanced endometriosis, which is frequently associated with adhesions, ovarian endometriomas, and tubal obstruction. Ovarian responsiveness to hyperstimulation plays a crucial role in determining the success rate of IVF. There are currently insufficient data to clarify whether the endometrioma-related damage to ovarian responsiveness precedes or follows surgery. Elucidation of this point is of utmost interest since it would strongly impact on the decision of whether to operate on women with endometriomas and who are selected for IVF. At present, there appears to be evidence supporting both an endometrioma-related injury and a surgery-mediated damage. The physiological mechanisms leading to ovulation are abnormal in ovaries with endometriomas.