Endometriosis is associated with infertility; however, the etiology of this association is unclear, thus complicating management. Several mechanisms of pathogenesis have been proposed; however, no one theory has been implicated. Medical therapy can be helpful in managing symptoms, but does not improve pregnancy rates. The role of surgical treatment remains controversial. There is little data regarding ovulation induction treatments for endometriosis only, whereas superovulation with intrauterine insemination has shown modest improvement in pregnancy rates in women who may have endometriosis. The most effective treatment for endometriosis-associated infertility is in vitro fertilization. Recent focus on proteomics and genetics of the disease may aid in optimizing treatment options.