In the modern world, various forms of stressful conditions are an important problem for human health. The prolonged stress experienced by residents of large cities can lead to a decrease in cognitive functions, causes the development of anxiety disorders, depressive states, as well as more serious diseases. Studying the effect of stress and its consequences on the human body, as well as the development of anti-stress drugs, are priority tasks for modern science. The changes in the functioning of genes are the molecular genetic factors of stress manifestations; however, the mechanisms by which stress affects the functioning of genes are not fully understood. Analysis of the transcriptome underlies the study of gene functioning and is one of the most effective approaches to studying the mechanisms that determine the development of stress conditions and ways to achieve anti-stress effects of drugs. It has now been established that in response to pathological effects not only information RNAs (mRNAs) are involved, but also various types of non-coding RNAs, in particular, microRNAs and long non-coding RNAs (lncRNAs). Recently, the idea that lncRNAs can interact with microRNAs and inhibit their activity is actively developing. Such functions are attributed to a new and actively studied type of RNA of circular nature (circRNAs). Recently, it has become apparent that the analysis of regulatory interactions «non-coding RNAs-mRNAs» is an important component for a detailed study of the mechanisms of pathogenesis and stress-induced disorders. This review presents the latest data on the role of mRNAs and non-coding RNAs in acute stress, as well as under the action of anti-stress drugs.