The paper considers the problem of solving the inverse problem of retrieval of the vertical distribution of atmospheric temperature from a Rayleigh scattering lidar signal in a high spectral resolution lidar. It is shown that the lidar signal, filtered from the aerosol scattering signal using a molecular filter, acquires a parasitic dependence on the atmospheric temperature due to a change in the width and shape of the Rayleigh scattering line contour. Signal distortions have a significant effect on the result of retrieval of the vertical temperature distribution and do not allow using the standard signal processing technique. To eliminate the influence of the signal filtering effect, the advanced temperature retrieval algorithms should be applied.