The aim was to investigate ventricular myocardial functions in patients with type II diabetes mellitus (DM) with cardiovascular autonomic neuropathy (CAN) in correlation with serum N-terminal pro-brain natriuretic peptide (NT-pro-BNP). We studied 56 patients with type II DM of >5 years' duration. Thirty healthy subjects matched for age and sex served as control group. The patients with type II DM were divided into two groups according to the outcome of the autonomic nerve function tests as those with CAN (DM + CAN) and without CAN (DM). Echocardiographic studies were performed to assess ventricular functions. NT-pro-BNP levels were measured in all patients. Subclinical left ventricular diastolic dysfunction was not different between diabetic patients with CAN (84 %) and those without CAN (74.2 %); all of them were classified as impaired relaxation pattern (p > 0.05). Subclinical right ventricular diastolic dysfunction was not also different between diabetic patients with CAN (48 %) and those without CAN (32.3 %) (p > 0.05). The NT-pro-BNP levels were not different between patient groups and not significantly increased in patients with diastolic dysfunction. Multivariate logistic regression analysis demonstrated that only diabetes mellitus was associated with diastolic dysfunction (OR 5.8, 95 % CI 1.7-19.2, p = 0.004). NT-pro-BNP is not significantly elevated in diabetic patients with subclinical mild diastolic dysfunction which is not related to CAN.