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The Heliogeophysical Complex of RAS, which is developing at the Institute of Solar-Terrestrial Physics SB RAS in the Irkutsk region, includes instruments for studying the Sun, the upper atmosphere and the mesostratospheric lidar system (MS lidar) for analyzing the neutral part of the atmosphere from Earth’s surface to the thermosphere (100–110 km altitude). More specifically, the objective of the MS lidar is to measure profiles of thermodynamic parameters of the atmosphere and the altitude distribution of the aerosol-gas composition. To solve these problems, the MS lidar ensures the use of several laser sensing methods at a number of specially selected laser wavelengths in the total range 0.35–1.1 μm. In this case, the following types of scattering are used: molecular, aerosol, Raman, resonance, as well as differential absorption, Doppler broadening and shift of the spectrum of scattered radiation. The article describes the methods used in the MS lidar and the measured atmospheric characteristics.