The paper describes an original method for analysis of the peripheral blood flow oscillations measured with the laser Doppler flowmetry (LDF) technique. The method is based on the continuous wavelet transform and adaptive wavelet theory and applies an adaptive wavelet filtering to the LDF data. The method developed allows one to examine the dynamics of amplitude oscillations in a wide frequency range (from 0.007 to 2 Hz) and to process both stationary and non-stationary short (6 min) signals. The capabilities of the method have been demonstrated by analyzing LDF signals registered in the state of rest and upon humeral occlusion. The paper shows the main advantage of the method proposed, which is the significant reduction of ‘border effects’, as compared to the traditional wavelet analysis. It was found that the low-frequency amplitudes obtained by adaptive wavelets are significantly higher than those obtained by non-adaptive ones. The method suggested would be useful for the analysis of low-frequency components of the short-living transitional processes under the conditions of functional tests. The method of adaptive wavelet filtering can be used to process stationary and non-stationary biomedical signals (cardiograms, encephalograms, myograms, etc), as well as signals studied in the other fields of science and engineering.