Considered modern system of automatic microscopic analysis (SAMA), based on the technology of automatically generating digital models of specimens. Considered the main function of such systems, focused on analysis of morphology and biomarkers of a wide range of specimens, including functions of download and identification, mapping, adaptation to the individual characteristics of the specimen, formation of digital copy of the specimen and its analysis. Considered automatic stages of SAMA work and interactive control of SAMA when performing analyses of various types. Given the characteristics of some SAMA of different producers. Estimations of efficiency of SAMA application compared to manual microscopy and automatic analyzers of other types are given.