Endometriosis has been one of the most confusing gynecological diseases since it was first described. Whereas there is a reasonable body of evidence in literature to demonstrate an association between endometriosis and infertility, a definite cause and effect relationship has not been established. The mechanism by which endometriosis causes infertility remains an enigma. Virtually every aspect of reproduction in women with endometriosis has been investigated and purported to be impaired. Impairment of implantation and pregnancy rates seems to affect women with endometriosis. Whether this is due to poor quality embryos derived from impaired oocytes or endometrial defects or both has been argued. Structural abnormalities of the uterine wall and tube in women with endometriosis have also been described by other researchers. Adding more confusion to this topic is the altered immune function and the peritoneal environment and their detrimental effects on the sperm motility and morphology. This uncertain pathophysiology has resulted in the lack of consensus on the treatment of endometriosis-associated infertility. The aim of this review is to describe the current pathophysiology of endometriosis-related infertility, how laparoscopic surgery may influence fertility rates.