The study was aimed to the biological effectiveness of the proton scanning beam of the first Russian medical facility. The clonogenic assay of B-16 tumor cells was used as a test system. Cell irradiation was carried out in a suspension condition in a water phantom. Single and three-field exposures were studied. The dose interval was 2-8 Gy. The energy range from 47.5 to 92.0 MeV was used for the Bragg peak formation. The relative biological effectiveness of protons comparing to gamma-rays was 1.2 for single-field and 1.5 for three-field irradiation. The results obtained agree with literature data related to the used cell culture (B-16) and linear energy transfer range (3÷8 keV/µm)