MicroRNAs, small non-coding RNAs expressed by eukaryotic cells, play pivotal roles in shaping cell differentiation and organism development. Deregulated microRNA expression is associated with several types of diseases including cancers, immune disorders and infection. Acting at the post-transcriptional level, miRNAs have expanded our understanding of the control of gene expression in regulatory networks involved in the adaptation to environmental situations such as biotic stress. It is increasingly clear that miRNAs are an important part of the host response to microbes. This review presents the current state of knowledge about the role of miRNAs in the response to both bacterial pathogens and commensal bacteria in human cells or animal experimental models. Some microRNAs, including miR-146, miR-155, miR-125, let-7 and miR-21, are commonly affected during bacterial infection and contribute to immune responses protecting the organism against overwhelmed inflammation. Cell-specific relationships between miRNAs and their targets are also engaged in the alterations induced by virulent bacteria in the proliferation/differentiation/apoptosis pathways of their host cells. In a separate role, miRNA modulation also represents a mechanism through which commensal bacteria impact the regulation of the barrier function and intestinal homeostasis.