The Salair fold-nappe terrane (a.k.a. Salair orogen, Salair) is the northwestern part of the Altai-Sayan folded area of the Central Asian Orogenic Belt. It is composed of Cambrian – Early Ordovician volcanic rocks and island-arc sedimentary deposits. In plan, Salair is a horseshoe-shaped structure with the northeast-facing convex side, which is formed by the outcrops of the Early Paleozoic folded basement. Its inner part is the Khmelev basin composed of Upper Devonian – Lower Carboniferous sandstones and siltstones. The Early Paleozoic volcanic rocks and sediments of Salair are overthrusted onto the Devonian-Permian sediments of the Kuznetsk basin. The Paleozoic thrusts, that were reactivated at the neotectonic stage, are observed in the modern relief as tectonic steps. Our study of the Salair deep structure was based on the data from two profiles of magnetotelluric sounding. These 175-km and 125-km long profiles go across the strike of the Salair structure and the western part of the Kuznetsk basin. Profile 1 detects a subhorizontal zone of increased conductivity (100–500 Ohm·m) at the depths of 8–15 km. At the eastern part of Profile 1, this zone gently continues upward, towards a shallow conducting zone that corresponds to the sediments of the Kuznetsk basin. Two high-resistance bodies (1000–7000 Ohm⋅m) are detected at the depths of 0–6 km in the middle of the section. They are separated by a subvertical conducting zone corresponding to the Kinterep thrust. The main features are the subhorizontal positions and the flattened forms of crustal conductivity anomalies. At the central part of Profile 2, there is a high-resistance block (above 150000 Ohm⋅m) over the entire depth range of the section, from the surface to the depths of about 20 km. In the eastern part of Profile 2, a shallow zone of increased conductivity corresponds to the sediments of the Kuznetsk basin. The subhorizontal mid-crust layer of increased conductivity, which is detected in the Salair crust, is typical of intracontinental orogens. The distribution pattern of electrical conductivity anomalies confirms the Salair thrust onto the Kuznetsk basin. The northern part of the Khmelev basin is characterized by high resistivity, which can be explained by abundant covered Late Permian granite massifs in that part of the Khmelev basin. The Kinterep thrust located in the northeastern part of the Khmelev basin is manifested in the deep geoelectric crust structure as a conducting zone, which can be considered as an evidence of the activity of this fault.