Abstract Background This study describes a new method for determining site-specific vascular shear stress using dynamic measures of shear rate and blood viscosity (BV) in the carotid arteries, and examines characteristics of carotid arterial shear stress among patients with lacunar infarction. Methods Vascular shear stress measurements were conducted in 37 patients (17 lacunar infarction patients and 20 control subjects) using duplex ultrasonography. Vessel wall diameters and velocities were measured in each arterial segment at peak-systolic (PS) and end-diastolic (ED) phases, for calculation of PS/ED shear rates. PS/ED shear stresses [dyne/cm 2 ] were determined with PS/ED shear rates and shear-rate dependent BV values. For comparison, both values of hematocrit-derived BV and BV measurements at 300 s -1 were used for calculation of shear stress. Results All cardiovascular disease (CVD) risk factors including BV values were similar between the two groups. In both common carotid arteries, PS and ED shear stresses were significantly lower in the patients with lacunar infarction than in controls in multivariate models that included age, sex, and other major CVD risk factors. PS and ED shear stresses using the shear rate specific BV were 4.5% lower and 7.3% higher than those using the two other BVs, respectively. Conclusion Lacunar infarction was associated with reduced carotid arterial shear stress. The use of estimated BV for calculating carotid arterial shear stress provides more accurate assessment of the hemodynamic contribution of shear stress than previous models that have arbitrarily assigned a constant value to this dynamic flow property.