An increasing number of studies indicates the central role played by the intestinal microbiota on the peripheral and central nervous system. Indeed, it has been shown that not only bacterial-derived products can influence the perception of pain, but also perturbations in microbiota (or dysbiosis) are often associated with intestinal or extra-intestinal pathologies such as neurodegenerative or developmental disorders. In this review, we present the preclinical and clinical studies highlighting the impact of the microbiota on the perception of pain in different pathological contexts.We discuss the cellular and molecular mechanisms by which intestinal microbiota modulate “pain-sensing” sensory neurons at the periphery, and the overall impact of the brain/gut/microbiota axis in the control of aversive painful behaviors and neurological disorders. Finally, we discuss the direct host/microbiota interaction which involves the activation of nociceptors by microbeassociated molecular patterns (MAMPs). Thus, new studies on the interaction between the microbiota and the nervous system should lead to the identification of microbial ligands and drugs targeting host receptors, which could ultimately improve the management of chronic pain and “well-being”.