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In this paper, wall shear stress (WSS) in rat common carotid arteries is numerically determined by pulsatile blood flow rate and vessel radius. The WSS is then decomposed into the Intrinsic Mode Functions (IMFs) by Empirical Mode Decomposition (EMD) proposed by Huang et al. in 1998. The mean frequencies and energy densities of the IMFs are computed and analyzed. It is shown that EMD of WSS in the rat common carotid arteries acted as a filter bank of λth order, where λ ~ 1.5 - 1.9 and the values of λ for Spontaneously Hypertensive Rats (SHRs) are larger than those for Wistar Kyoto rats (WKYs) at ages of 12w and 18w, respectively. The λ might be an index reflecting the intrinsic frequency characteristics of WSS. In contrast to Fourier spectra of WSS, the EMD spectra are more appropriate to differentiate the frequency characteristic of WSS signals between SHRs and WKYs. These results show a new view of frequency content of arterial WSS, which might be useful for the study of the blood-flow induced arterial remodeling.