Rationale: Ovarian endometriosis is a progressive disease with growing prevalence and severity. Therefore, the development of robust non-invasive laboratory screening methods for early diagnosis on the out-patient basis seems quite relevant. Aim: To assess a potential of the quantitative phase imaging technique for early diagnosis of ovarian endometrial cysts and post-operative relapses of the disease. Materials and methods: We analyzed 1578 nuclei of the peripheral blood lymphocytes from 82 patients with ovarian endometrial cysts, aged 21 to 37 years (mean age 26.4 ± 3.6 years). The patients were follow-up in a gynecology out-patient clinic (the town of Yessentuki, Russia). Assessments were made longitudinally, i.e., before a laparoscopic cystectomy, at 6 and 12 months in the post-operative period with or without treatment with dienogest-containing agents. Morphological and functional status of the nuclei from the peripheral blood lymphocytes was assessed in the real-time mode by quantitative phase imaging (QPI) with the phase-interference microscopy module of the Bioni hardware and software complex (Westgrade Ltd., Moscow) for clinical and laboratory diagnostics, and the morphodensitometric segmentation technology. Results: The comparative analysis of morphometric parameters of CD3<sup>+</sup> cells taken from peripheral blood of healthy non-pregnant women and patients with ovarian endometrial cysts before surgery showed a significant increase of the calculated functional activities of the lymphocyte nuclei (0.898 vs 0.783, p < 0.05). Assessment of changes overt time in the differential diagnostic criteria of the nuclear response in the peripheral blood lymphocytes from patients with endometrial ovarian cysts showed the following. Compared to the parameters obtained before treatment, at 6 and 12 months of the post-operative period the relative intensity of nuclear segments (ΔI) decreased by 10.3 and 14.7, 10.6 and 12.9% in the group treated with and without dienogest, respectively. Relative distance between the centers of the nuclear segments (ΔL) demonstrated a trend towards an increase by 0.6 and 0.9, 4.2 and 2.1%. The numbers of nuclear segments increased by 18.3 and 13.4, 27.4 and 16.9%, whereas the nuclear perimeter decreased by 13.9 and 12.6, 11.9 and 7.8%, respectively. In the patients treated with dienogest, the rate of non-relapse at 6 and 12 months of the follow-up was 100%, whereas in the patients without dienogest therapy, 97.5 and 93.5%, respectively. Discussion: Interphase chromatin is a unique biosensor of the early abnormalities in a lymphoid cell. Modification of its structure and packaging density not only indicate changes of the morphofunctional status of the lymphocyte, but can be projected to the body as a whole and used for early pre-clinical diagnosis, assessment of severity of the pathological process and prediction of the outcome in various critic states. Conclusion: Practical implementation of QPI for clinical monitoring of patients with ovarian endometrial cysts makes it possible to obtain important information on the cell immunity in real time. It opens new opportunities to assess the efficacy of treatment and rehabilitation activities, as well as for early pre-clinical diagnosis of relapsing disease.