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The results of the study of the deep structure of the lithosphere in Eastern Siberia are presented. Based on data on the thickness of the permafrost ice horizon, gravity anomalies, geomagnetic field anomalies and seismological data, a model of the structure of the lithosphere of regions with a stable ice horizon thickness was obtained. It is shown that areas with large values of the thickness of the ice horizon gravitate towards the powerful roots of the lithosphere with increased density and magnetization. It has been suggested that the stability of permafrost horizons is provided by cold blocks of the lithosphere roots, which overlap the heat of the mantle. To search for endogenous causes of climatic risks in areas with accelerated degradation of permafrost, deep sections of the earth's crust were built. Analysis of data on the thickness of the ice horizon together with deep sections showed that fluid channels of deep vertical fault zones play a decisive role in the permafrost destruction process. Accelerated degradation of permafrost is localized near the outcrops of fluid-magmatic channels, where specific melting zones have been identified in the form of through taliks caused by endogenous factors of directional action under the influence of fluid flows rising from a depth of ~50–100 km. The studies carried out make it possible to understand the possible causes of the destruction of infrastructure in the permafrost zone and to predict the location of the most probable areas of accelerated degradation.