Non-alcoholic fatty liver disease (NAFLD) is considered a risk factor for atherosclerosis. The aim of the present study was to investigate the association of the pulsatility index (PI) of basilar artery (BA) and carotid intima media thickness (IMT) in diabetic and non-diabetic NAFLD patients. We compared a group of 80 stroke-free, diabetic and non-diabetic NAFLD patients and a control group of 26 healthy subjects without NAFLD. We then evaluated the PI of the BA by transcranial Doppler ultrasonography, and carotid IMT. The PI was significantly higher in diabetic NAFLD patients than in controls (p<0.003). Carotid IMT and asymmetrical dimethylarginine (ADMA) levels were higher in NAFLD patients than controls respectively (p<0.003, p<0.04). The PI of the BA was significantly correlated with age (R=0.369, p<0.001), male gender (R=0.207, p=0.035), diabetes (R=0.332, p=0.001), carotid IMT (R=0.296, p=0.002) and ADMA (R=0.349, p=0.015). A multiple regression analysis was performed with PI as the dependent variable with known clinical risk factors. Age (beta=3.54, p<0.001), diabetes (beta=2.32, p=0.022), gender (beta=2.20, p<0.03), ADMA (beta=2.25, p<0.031), and carotid IMT (beta=2.41, p<0.017), were independent predictive factors of BA PI. Adjustment for age and gender did not alter these relative risks, exhibiting a significant independent contribution to PI. The increased PI observed in this study represents enhanced cerebrovascular resistance, and we observed that the age, male gender, diabetes, ADMA levels, and carotid IMT were independent predictive factors of BA PI.