Objective: Determination of expression levels of molecular genetic markers to improve the diagnosis of ovarian endometriosis (OE) and define prognostic criteria for recurrence and possible malignant transformation.Materials and methods: Expression levels of lncRNAs in 30 and 25 cases of ovarian endometriotic cysts and ovarian adenocarcinomas, respectively, as well as in 25 cases in the control group, were studied using molecular genetic testing.Results: Persistent increase in lncRNA MALAT1 expression level was found with the disease progression, and consistent increase and reduction of Linc-ROR expression level in the control group and in the group of patients with adenocarcinoma. For differential diagnosis of normal condition and OE, OE and adenocarcinoma, ROC curves for lncRNA expression levels were constructed, and important rule was derived to determine the histological status of the surgical material.Conclusion: According to the results of expression levels of lncRNA markers MALAT1 and Linc-ROR in the groups of patients with endometriosis, adenocarcinoma and in the control group, the assessment of their potential possibility for predicting these conditions was suggested. Further targeted research in this area is necessary to develop new prognostic markers for endometriosis-associated ovarian cancer and search for additional therapeutic targets.