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To determine the heterogeneity of the time-varying shear stress profiles in the human carotid bifurcation, a region prone to atherosclerosis.Lagrangian bicubic interpolation of phase-contrast MRI images was used to determine the shear stress profiles for three adult healthy male volunteers. Frequency spectra for the common and internal carotid artery (CCA and ICA, respectively)-derived shear stresses were examined in order to determine the presence of significant heterogeneity in the intensity distribution.Hemodynamic characteristics (peak, minimum, average shear stress, and oscillatory shear index [OSI]) were highly heterogeneous both along the length of the vessel as well as circumferentially around the CCA and ICA. In the frequency domain, intensities below 4 Hz were significantly higher in the CCA compared to the sinus region of the ICA, indicating that shear stress heterogeneity can be detected in the frequency domain. The harmonic index, a measure of the relative contributions of dynamic and static components of the shear stress signal, colocalizes with OSI, which implies a relationship between specific frequency components and atherosclerosis development.These findings indicate that the time and frequency dependent parameters of in vivo shear stress have important implications for regional development of atherosclerosis.