OBJECTIVES: Endothelial dysfunction is an early event and a critical step in the pathogenesis of systemic sclerosis. Accurate and sensitive tests are needed to correctly assess the degree of microvascular endothelial dysfunction. Spectral analysis of skin blood flow contains a characteristic low frequency reported to be associated with endothelial function in healthy subjects. We hypothesized that the relative amplitude of the oscillation recorded for this low frequency spectrum (0.008 to 0.021 Hz) would be less pronounced in patients with systemic sclerosis than in healthy subjects and in patients with primary Raynaud's phenomenon. PATIENTS AND METHOD: Twenty-one patients with systemic sclerosis, twenty patients with primary Raynaud phenomenon and eleven healthy subjects were enrolled. Skin perfusion was recorded at rest for 30 minutes using laser Doppler flowmetry on the pad of the left third left. Fourier transform spectral analysis was applied to obtain the mean amplitude of the cutaneous blood perfusion signal of the total spectrum from 0.008 to 1.6 Hz and the mean amplitude of each characteristic frequency in the laser Doppler flowmeter blood flow oscillations. RESULTS: The relative amplitudes of each characteristic frequency in the laser Doppler flowmeter blood flow oscillations were not statistically different in the three groups, particularly for frequency spectrum from 0.008 Hz to 0.021 Hz. CONCLUSION: Fourier transform spectral analysis of baseline cutaneous blood flow does not provide significant information. Further studies are required, perhaps using wavelet spectral analysis or stimulated conditions.