Mycobacterium tuberculosis causes an infection in humans with clinical manifestations varying from asymptomatic carrying of bacteria to rapidly progressing tuberculosis. The range of clinical manifestations depends on complicated and still poorly understood interactions between pathogenic bacteria and the host. Changes in gene expression that result from the immune response of the host are necessary for the survival and function of M. tuberculosis. This review is devoted to the analysis of the dynamic changes in the transcriptome of M. tuberculosis occurring in the course of an infection in the host organism tissues. We reviewed the modern data on changes in transcriptome, obtained in various model systems. A large part of this review is devoted to the description of the changes in the biochemistry of the infectious process caused by M. tuberculosis during the transition from initial infection, through latency, to reactivation of the pathogen. We also discuss the changes in gene expression occurring at each stage and alterations in bacterial metabolism caused by them.© Pleiades Publishing, Ltd., 2012.