Abstract Background and Aims: Cardiac autonomic neuropathy (CAN) in type 2 diabetes mellitus (T2DM) is one of the independent risk factor for cardiovascular mortality. The aim of the study was to analyze the effect of long-chain w-3 polyunsaturated fatty acids (w-3 PUFA) on the levels of N-terminal pro-brain natriuretic peptide (NT-proBNP) and on some lipid profile parameters in patients with T2DM and CAN. Material and Methods: 36 patients with T2DM and verified CAN were divided into 2 groups. The first group received traditional hypoglycemic therapy (n = 15, control) for three months; patients in group 2 (n = 21) received in addition 1 g/day of the long-chain w-3 PUFA for three months. Results: Prescription of the w-3 PUFA to the patients with T2DM and СAN was accompanied by a statistically significant decrease of NT-proBNP level and led to significantly positive changes in the high density lipoprotein cholesterol and triglycerides levels in the blood. Conclusions: Obtained results suggest that the efficacy of w-3 PUFA is the result of a direct effect of the pharmacological agent on the investigated indexes