Endometriosis is a common gynecologic disorder with an enigmatic etiopathogenesis. Although it has been proposed that endometriosis is a hormonal disease, an autoimmune disease, a genetic disease, and a disease caused by exposure to environmental toxins, our understanding of its etiopathogenesis is still inadequate, as reflected by recent apparent setbacks in clinical trials on endometriosis. In the last 5 years, evidence has emerged that endometriosis may be an epigenetic disease. In this article, the evidence in support of this hypothesis is reviewed, and its diagnostic, therapeutic and prognostic implications discussed. Publications, up to the end of June 2009, pertaining to epigenetic aberration in endometriosis were identified through PubMed. In addition, publications on related studies were also retrieved and reviewed. Epigenetics appears to be a common denominator for hormonal and immunological aberrations in endometriosis. Epigenetics also appears to have a better explanatory power than genetics. There is accumulating evidence that various epigenetic aberrations exist in endometriosis. In vitro studies show that histone deacetylase inhibitors may be promising therapeutics for treating endometriosis. In conclusion, several lines of evidence suggest that epigenetics plays a definite role in the pathogenesis and pathophysiology of endometriosis. As such, endometriosis is possibly treatable by rectifying epigenetic aberrations through pharmacological means. DNA methylation markers may also be useful for diagnostic and prognostic purposes. It is also possible that the delineation of the epigenetic changes accompanied by the genesis and progression of endometriosis could lead to interventions that reduce the risk of developing endometriosis.