The article contains the results of a study of two different methods for calculating the spectral parameters of laser Doppler flowmetry in patients with diabetic microangiopathy caused by type 2 diabetes mellitus (main group) and those with excluded diabetes mellitus (control group). Spectral indices were calculated using either average or maximum amplitudes of the frequency ranges. When comparing the contribution of respiratory and pulse fluxmotions using average amplitudes, there were significant (p < 0.05) differences between the main and control groups. On the contrary, when using the maximum amplitudes, no significant differences were noted (p > 0.05). Also, significant correlations were found between the contributions of respiratory and pulse fluxmotions and the estimated glomerular filtration rate in the main group, using both calculation methods. These studies indicate the feasibility of using a technique based on the analysis of average amplitudes to increase the specificity of laser Doppler flowmetry as a method for diagnosing diabetic microangiopathy.