We isolated and characterized cell cultures from eutopic endometrium and endometriotic lesions of women with malformations of the internal reproductive organs. The cells had fibroblast-like shape and intensively expressed CD90, CD73, CD105, CD44, CD146, and CD117 and were capable of induced adipogenic and osteogenic differentiation in vitro . The obtained cultures exhibited properties of multipotent mesenchymal stromal cells; at the same time, they demonstrated in vitro immunophenotypic differences from cell cultures of eutopic and ectopic endometrium of women without developmental abnormalities, which suggests their functional difference. The cells from eutopic endometrium and from ectopic endometriotic lesions can be used as the model for studying of the etiology and pathogenesis of endometriosis and for testing new drugs for this specific group of patients. Markers CD90 and CD117 were identified as promising molecules for the development of minimally invasive diagnostics of endometriosis based on cell cultures from eutopic endometrium.