This review considers modern strategy of whole-transcriptome investigation of intracellular pathogens in vivo. The methods of preliminary enrichment for bacterial RNA are discussed in details, including hybridization-based approaches and the peculiarities of cDNA synthesis in bacteria; methods of synthesizing cDNA from the view of features of prokaryotic RNAs and methods of bacterial cDNA analysis are also described, including high-throughput RNA-seq. The discussed methods are exemplified by analysis of Mycobacterium tuberculosis in different infection models: in cell lines, infected animal tissues and organs, and human surgical samples of lung. The advantages and limitations of different methodological approaches are discussed.