This study examines the effect of the procedures used in three different probabilistic seismic hazard analysis (PSHA) methods for estimating the rates of exceedance of ground motion. To evaluate the effect of these procedures, the Cornell–McGuire and Parametric-Historic methods, and the method based on Monte Carlo simulations are employed, and the seismic source model, based on spatially smoothed seismicity, is used in the calculations. Two regions in Russia were selected for comparison, and seismic hazard maps were prepared for return periods of 475 and 2475 years. The results indicate that the choice of a particular method for conducting PSHA has relatively little effect on the hazard estimates. The Cornell–McGuire method yielded the highest estimates, with the two other methods producing slightly lower estimates. The variation among the results based on the three methods appeared to be virtually independent of the return period. The variation in the results for the Sochi region was within 6%, and that for the Kamchatka region was within 10%. Accordingly, the considered PSHA methods would provide closely related results for areas of moderate seismic activity; however, the difference among the results would apparently increase with an increase in seismic activity.