We statistically investigated whether the impact of cardiovascular risk factors on arterial stiffness would be different from that on arterial wall thickness. We analyzed 1648 Japanese type 2 diabetic patients. Arterial stiffness was evaluated by pulse wave verbosity (PWV) and wall thickness was assessed with carotid intima-media thickness (IMT) by ultrasonography. We developed a common regression model to PWV and IMT by extending the linear mixed model and statistically detected the difference in the impact of cardiovascular risk factors between the two indices. There was a significant correlation between PWV and IMT (r=0.365, p < 0.001). Sex, diabetic duration, hemoglobin A1c levels, and the presence of retinopathy and cardiovascular disease were comparable independent risk factors for elevated PWV and IMT. On the other hand, the impact of age, systolic blood pressure, and low- and high-density lipoprotein cholesterol levels were significantly different between the two measurements (all p < 0.05). Cholesterol levels were significantly associated with IMT but not with PWV. Age and systolic blood pressure had a significant impact on both measurements, but the impact on PWV was significantly greater than that on IMT. Indeed, patients with low IMT but with advanced age and high systolic pressure had high PWV, whereas patients with low PWV but with impaired cholesterol levels had high IMT. The extended linear mixed model statistically confirmed that the impact of cardiovascular risk factors on elevated PWV and IMT were not identical in Japanese patients with type 2 diabetes mellitus.