The understanding of bacterial pathogenesis is dependent on techniques that elucidate the underlying genetic and biochemical mechanisms. To study the mechanism of bacterial survival and proliferation within host cells we need accurate tools that tell us what is occurring within the infecting organism. It has now become possible to determine the transcriptional status of in vivo-derived bacteria at the level of the whole genome. Such expression profiles serve as a monitor of the host cell environment as well as an indicator of the bacterial adaptation to its intracellular niche. Here, we review the methods used to produce microarray data for defining the bacterial intracellular transcriptome, and examine the pitfalls in extracting bacterial RNA from the infected host compartment.