Three different methods in combination with integration of differences in signals were applied for EEG analysis to distinguish changes in EEG caused by microwave: S-parameter, power spectral density and length distribution of low variability periods. The experiments on the effect of modulated low-level microwaves on human EEG were carried out on four different groups of healthy volunteers exposed to 450 MHz microwave radiation modulated with 7 Hz, 14 Hz, 21 Hz, 40 Hz, 70 Hz, 217 or 1000 Hz frequencies. The field power density at the scalp was 0.16 mW/cm2. The EEG analysis performed for individuals with three different methods showed that statistically significant changes occur in the EEG rhythms energy and dynamics between 12% and 30% of subjects.