The aim of this study is to scrutinize the ability of principal component analysis (PCA) over power spectral densities (PSD) for common femoral artery blood flow study. Doppler femoral artery signals of patients with occluded arteries and of healthy subjects were recorded. Then, power spectral densities of these signals were obtained using the Welch method. To clearly determine the difference between the groups of occluded patients and healthy subjects, PCA was implemented with patients and healthy matrices derived from PSD. The basic differences between the healthy and occluded patients were acquired with 1st principal component. The use of PCA of physiological waveforms is presented as a powerful method likely to be incorporated into future medical signal processing.