The study of deep continental boreholes revealed significant vertical variations in heat flow. This fact still has no satisfactory explanation. One possible cause could be the effects of past climate changes, namely changes in the Earth's surface temperature. The paper discusses some consequences of accounting for the influence of paleoclimate on the measured heat flow using the example of the platform part of the Republic of Bashkortostan. A numerical simulation of the influence of paleoclimate on the distribution of the thermal field in the borehole was performed using two models of past climate changes. The first model, adopted earlier, includes two major climatic episodes of the past, the Würm glaciation 80–10 thousand years ago, and the Little Ice Age, 600–150 years ago. The second model uses the climatic curve for the Meso-Cenozoic, which additionally takes into account the warming that began about 65 Ma, reached its maximum about 45 Ma, and followed by a cooling that continued with some fluctuations until the present time [Velichko, 1987]. It is shown that, in the analysis of vertical variations in heat flow, the use of a model of past climate changes, taking into account more distant large climatic events than has been done previously, allows us to estimate the paleoclimate influence as much more significant than previously thought. However, at this stage of the research, with the accepted models of temperature changes at the Earth's surface, the vertical variations of the heat flow established by the results of experimental geothermal studies cannot be explained only by the influence of the paleoclimate. To solve the problem, we need a detailed study of the thermophysical properties of rocks, high-quality temperature measurements in wells, and improvement of the model of past climate changes in the region under study.