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The possibility of compensating the atmospheric influence on precision measurement of gravitational ‘‘redshift’’ using the Earth orbiting satellites is discussed. For a communication radio signal propagating from a ground-based tracking station to a spacecraft and back, the interaction with the ionosphere and the troposphere produces a undesirable contribution to the total frequency shift which must be removed by specific data processing. In the paper we present a brief overview of atmospheric hindrances with estimation of their magnitudes. Then, the algorithms for filtering the gravitational effects against the atmospheric noise background are considered. The efficiency of such filtering is illustrated using the example of gravitational measurements with Spectr-R satellite in the RadioAstron mission.