Sequencing-based studies have illuminated increased transcriptional complexity within the genome structure of bacteria and have resulted in the identification of many small regulatory RNAs (sRNA) and a large amount of antisense transcription. It remains an open question whether these sRNAs all indeed play regulatory roles, but their identification led to an exponential increase in studies searching for their function. This allowed to show that sRNAs may modulate virulence gene expression, cellular differentiation, metabolic functions, adaptation to environmental conditions and pathogenesis. In this review we will provide mechanistic insights into how sRNAs bind mRNAs and/or proteins. Furthermore, the important roles of the RNA chaperone Hfq, the CsrA system and the CRISPR RNA will be discussed. We will then focus on sRNAs and 5(') untranslated region (UTR) elements of intracellular bacteria like Chlamydia, Listeria, Legionella, or Salmonella, and place emphasis on those that are expressed during replication in host cells and are implicated in virulence and metabolism. In addition, sRNAs that regulate motility, iron homeostasis, and differentiation or stress responses will be highlighted. Taken together sRNAs constitute key elements in many major regulatory networks governing the intracellular life and virulence of pathogenic bacteria.