AIM: This research was designed to study the temporal changes in cardiovascular autonomic regulation, assessed by 24-hour heart rate (HR) variability, and the possible relation of changes in HR variability to cardiovascular risk factors and progression of coronary artery disease (CAD) among type II diabetic subjects.METHOD: In a single-center substudy of The Diabetes Atherosclerosis Intervention Study (DAIS), 53 patients assigned to fenofibrate (n = 26) or placebo (n = 27), underwent time and frequency domain and fractal analysis of HR variability, coronary risk variable analyses and quantitative coronary angiograms at baseline and after three years' follow-up. RESULTS: Twenty-four hour standard deviation of sinus intervals (SDNN) decreased from 113 ± 35 to 94 ± 30 msec (P < 0.001) during the three year period. Low frequency power spectral component and short-term fractal scaling exponent also decreased (P < 0.001 and P < 0.05, respectively). The reduction of SDNN was weakly related to a change in the triglyceride level (r = −0.33, P < 0.05), glucose level (r = −0.28, P < 0.05) and total cholesterol concentration (r = −0.35, P < 0.01). Furthermore, the reduction of SDNN was related to a decrease in the minimum lumen and mean segment diameter of the coronary arteries (r = 0.36, P < 0.01, and r = 0.39, P < 0.01, respectively). This association was more marked in the placebo group (r = 0.50, P < 0.01 and r = 0.44, P < 0.05, respectively) than among the patients randomized to fenofibrate (not significant for both). CONCLUSIONS: Cardiovascular autonomic regulation assessed by HR variability deteriorates rapidly in type II diabetic subjects with CAD during the time course. Impairment in HR variability is associated with changes in common coronary risk variables and with a progression of CAD.