We examined the relationship between the coefficient of variation in the R-R intervals (CVR-R) using electrocardiograms and the ultrasonic intima-media thickness (IMT) of the carotid artery, an atherosclerotic parameter, in type 2 diabetes mellitus (DM) patients with diabetic neuropathy (n=47, males/females: 29/18; mean age: 62 years). In this study, the CVR-R-related indexes, including CVR-R at rest (CVR-R_rest), CVR-R with deep breaths (CVR-R_breath) and their difference (CVR-R_breath minus CVR-R_rest: CVR-R_dif), were defined. Data such as body mass index, smoking habits, hemoglobin A1c, blood pressure, and serum low-density lipoprotein were collected. A significant inverse correlation was observed between max-IMT and CVR-R_dif (β=–0.34, p =0.042), but not CVR-R_rest or CVR-R_breath, in multivariate analyses adjusted for all the data. Therefore, the CVR-R_dif may serve as a clinical index for the diabetic autonomic neuropathy-atherosclerosis relation in type 2 DM patients.