Endometriosis is a common gynecological disease which mainly affects women of reproductive age. It is defined by the presence and growth of ectopic endometrial tissue which has the histological characteristics of the normal endometrium. The precise aetiology of endometriosis remains unclear. Accumulating evidence suggests that various epigenetic aberrations may play an essential role in the pathogenesis of endometriosis, such as DNA methylation, synthesis of small non-coding RNA, and histone modification. DNA methylation is one of the most common DNA modification and it represents the covalent bonding of the methyl group to the fifth carbon atom of the cytosine in the CpG dinucleotides. Methylation of the gene promoter region leads to its suppression. MicroRNAs regulate gene expression at the posttranscriptional level by specifically binding to the 3'-untranslational region of targeted mRNA and downregulate the expression of specific proteins. At least eight patterns of histone modification have been identified, with acetylation being the most intensively studied. „Global“ histone acetylation is related to transcriptional activity. Variations in the epigenetic patterns of genes known to be involved in the aberrant hormonal, immunologic, and inflammatory status of endometriosis have been observed. Thus, hypomethylation of ERβ, aromatase gene and SF-1, and hypermethylation of PR-B promoter regions, coding genes for histone deacetylase inhibitors and DNMTs are typical for endometriosis. Nonetheless, it is still unclear whether these molecular changes are the cause or consequence of the disease. The aim of this review is to present an overview and analyze so far known epigenetic alterations in endometriosis because, in the future, this alterations may constitute therapeutic targets for pharmacological compounds able to modify the epigenetic code.