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Aim. To analyze the expression of key apoptosis (Bcl-2, caspase-3) and autophagy (Beclin 1, Vps34, p62 and LC3) proteins regulators in peripheral blood T-lymphocytes of patients with systemic lupus erythematosus. Methods. The object of the study was peripheral blood T-lymphocytes of healthy donors and patients with systemic lupus erythematosus. To obtain T cells, we used the immunomagnetic separation method. Protein expression was analyzed using the Western blot method. Statistically analyzing the results was performed using the R software environment. The data was represented using boxplots. Groups were compared using the MannWhitney test. Results. According to the results of the study of the apoptotic proteins, we found an increased content of caspase-3 and the absence of significant changes in the content of the anti-apoptotic protein Bcl-2 in patients with lupus, which indicates active apoptotic activity. A comparative analysis of Beclin 1 and Vps34 showed their increased content in the cells of patients, which indicates the activation of autophagy. The analysis of two isoforms of LC3 protein revealed their low content in the group of patients. Since the scatter of indicators was very different from the average value, we analyzed these indicators depending on the severity of the disease. In the acute course group, high content of protein LC3-I was detected, the content of form II was lower. In the group with the subacute course, the number of both isoforms is lower than in the other groups. In the group with a chronic course, significant increases of protein LC3-II and a decrease in the ratio of LC3-I/LC3-II were found. Conclusion. The study showed that depending on the severity of systemic lupus erythematosus, the content of protein LC3 isoforms changes, which can be used for differential diagnosis of disease forms.