We have observed 118 patients, including 64 patients with T2DM and NAFLD (I group), 26 patients with T2DM (II group) and 28 patients with NAFLD (III group). The control group consisted of 25 apparently healthy individuals. We have determined the quantitative content of lymphocyte subpopulations in peripheral blood, the concentration of cytokines (interleukin (IL) 1 beta, 2, 4, 6, 8, 10, 17, TNF-alpha and IFN-gamma) in peripheral blood serum and in coprofiltrates, and evaluated the state of the microbiota of the intestine as a result of bacteriological examination of faeces. The studies have found that each of the studied pathologies (T2DM, NAFLD and their combination) is characterized by its own cytokine status, which reflects both the presence of inflammatory processes and focus immunopathological reactions in the body. Identified changes in the levels of cytokines and lymphocyte subpopulation content in combination T2DM with NAFLD can be used both for diagnosis and for predicting adverse development of this disease, the intensity of the proliferation of connective tissue and the degree of fibrosis formation.