Endometriosis (EM) is a common disease in women of reproductive and perimenopausal age, characterized by the formation of ectopic foci of endometrial proliferation. The pathogenesis of the disease is multifactorial and has not been fully studied. Non-invasive examination methods have relative diagnostic value; therefore, current therapeutic approaches frequently do not provide a complete recovery. This situation determines the interest in studying the molecular and genetic background of EM and in searching for new diagnostic and prognostic markers. In this review, we briefly discuss the prevailing theories of EM etiology, taking into consideration modern scientific concepts. A separate chapter highlights the data of the genome-wide associative studies (GWAS) that indicate the possibilities of involving a number of genes in the pathogenesis of EM (WNT4, CDKN2BAS, FN1). The main part of the review is focused on the analysis of the gene expression studies comparing the ectopic and eutopic endometrium of women with EM. Considering the clinical significance, the results of three studies comparing expression profile of the eutopic endometrium of healthy women versus patients with EM are presented in detail. In conclusion, the prospects of the development and clinical application of heritable and expressed EM markers are assessed.