The microbiota-gut–brain axis is a complex and dynamic multi-directional ‘communication superhighway’ within the body including the central nervous system, the autonomic nervous system, the neuroendocrine and neuroimmune systems, the lymphatic system, the enteric nervous system and the gastrointestinal microbiota. The mechanisms of communication are slowly being unravelled and involve the main systems mentioned along with the by-products produced such as neuropeptides, neurotransmitter, hormones and immune modulators. Over the last decade increasing evidence points to an essential role of this axis in many fundamental neural processes and brain disorders. However, the limited clinical and preclinical studies do not clearly delineate a role for gut microbiota in the pathophysiology of pain state. The most researched area is in irritable bowel syndrome and in visceral pain studies in animal models. However, one cannot overlook the involvement of the microbiota in symptoms that are comorbid with chronic pain especially affective disorders. In this review we synthesise the available information highlighting the gut microbiota in visceral, inflammatory, and neuropathic pain states, including fibromyalgia, migraine, cancer and chemotherapy-associated pain. Given its part in many effector systems, there is a clear need for more focused investigations on the mechanism of action of the microbiota in human pain states, as current treatment strategies are often ineffective or provide limited relief.