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The effect of non-ionizing millimeter range electromagnetic waves (MM EMW) (30-300 GHz) on the bovine serum albumin (BSA) interaction peculiarities with acridine orange (AO) has been studied in vitro. The frequencies 41.8 and 50.3 GHz were chosen, since the first one is nonresonant frequency for the water, while the second one is resonant for water. The binding constant and number of binding sites were calculated at both irradiation presence and absence. AO was revealed to bind to BSA, while after the protein irradiation the interaction force strengthens. However, it was also shown that there are differences of the interaction parameters while irradiating by 41.8 or 50.3 GHz. AO binds to BSA, irradiated by MM EMW with the frequency 41.8 GHz much more weaker, than to that, irradiated by MM EMW with the frequency 50.3 GHz.