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The paper presents the results of a comprehensive analysis of geological research with data on the deep structure obtained by geophysical methods (seismic, electro-, magnetic, gravity, thermometric and seismological) for the territory of the Northern, Middle and Southern Tien Shan. The complex of geological and geophysical data indicates that in the deep parts of the Earth's crust of the modern Tien Shan there are many electrical, density and thermal inhomogeneities. The areas of junction of various tectonic segments are characterized by anomalies of increased electrical conductivity, are clearly manifested in the magnetic and gravitational fields and correspond to zones of deep faults. These zones are highly permeable and are zones of heat and mass flow and transport of fluids. To compare crustal and upper mantle inhomogeneities expressed in different geophysical fields, seismotomographic sections constructed on the basis of volumetric seismotomographic models at various spatial-scale levels, geoelectric and velocity sections along the profiles intersecting the main tectonic elements of the Tien Shan were analyzed. The most contrasting in terms of the difference in the velocities of P and S seismic waves are sections at depths of 0-5 km and 50-65 km, where the large-scale segmentation of the Tien Shan into the Northern, Southern and Western segments is most clearly traced. The upper crustal conductive layer and lenticular and other bodies of waveguides (at depths of 10–15 km) are possibly associated with cataclastic intrusions of granitoids, which are common in mountain-fold areas. The lower crustal conductor and the corresponding waveguide, sporadically appearing throughout the Tien Shan, apparently represent either a zone of increased plasticity or are caused by the presence of migma fields. The distribution of earthquakes clearly shows the zones of the Northern, Central and Southern Tien Shan and the segmentation of the Western and Central Tien Shan. Comparison of velocity anomalies in seismotomographic sections and objects of anomalously low electrical resistance in geoelectric sections of the Earth's crust indicates the existence of zones of increased fracturing or plasticity in the indicated intervals of the Earth's crust, as well as the coincidence of waveguides and zones of increased conductivity. The study was supported by the State Assignment of the Research Station of the Russian Academy of Sciences in Bishkek (AAAA-A19-119020190063-2).