Objective — determine the differences in the expression of miRNA and mRNA in the tissues of endometriomas and eutopic endometrium. Using bioinformatic analysis to evaluate the role of differentially expressed RNA in the pathogenesis of ovarian endometriosis. Material and methods. Analysis of microRNA transcriptome was performed by the sequencing method, the differences in mRNA expression were determined by micrometrical analysis. Evaluation of signaling pathways and processes were conducted by the enrichment of databases methods bioinformatic analysis. Results. Transcriptome analysis revealed significant differences in the expression of miRNA and mRNA in ectopic and eutopic endometrial tissues. It was found that the expression of miRNA and mRNA depends on the type of ovarian reserve (OVR): the greatest deviations in the expression were determined in patients with normal OVR, which may indicate an important role of hormonal control in the observed differences. Lists of target genes were obtained for identified miRNAs, which together with lists of differentially expressed genes were used for bioinformatic analysis of pathogenetic pathways and processes. The data obtained indicate the involvement of regulated target genes in the processes of proliferation, migration and invasion, in the key cascades of intracellular signaling and inflammatory processes. It was also found several ways involved in the processes of DNA repair and regulation of the mitotic cycle, which indicates the genotoxic effect of pathogenetic factors acting in the tissues of endometriomas. These factors can have a similar effect on adjacent ovarian tissues, which can lead to a decrease in ovarian reserve in endometriosis. Conclusion. The obtained data suggest that the change in the expression of microRNA in the tissues of the ectopic endometrium and the subsequent violation of the regulation of the expression of their target genes is an important pathogenetic link and can make a significant contribution to the development of endometriosis and associated reduction of the ovarian reserve.