Physiology of microorganisms is traditionally considered as one of branches of microbiology. Fundamental works in this field, the last of which were written almost 40 years ago, included such issues, as chemical composition, physico-chemical properties, metabolism, respiration, reproduction, and growth of microorganisms. For the last few decades, the main efforts of scientists in these fields were concentrated on decoding molecular-genetic mechanisms underlying functioning of microbial cells. At the same time, the accumulated scientific data in adjacent fields of biological science require insistently the necessity of new understanding and systematization of results of study of processes of vital activity of all species of living organisms, based on general integrative physiological principles. By the present time, it has been convincingly proved that the existence of higher organisms is impossible without constant interaction with the world of microbes and, hence, physiology of human, animals or plants is inextricably connected with physiological processes of their inhabiting microorganisms. In the present work the main actual problems of modern physiology of microorganisms are considered, and the necessity of separation of this branch of knowledge as an autonomous part of physiology is emphasized.