There is a growing appreciation that the gut microbiota plays a key role in maintaining homeostasis and that a disruption in its composition contributes to various disease states, including CNS disorders.The concept of a microbiota–gut–brain axis, although debated, is emerging to capture the importance that the microbiota has on regulating bidirectional gut–brain communication pathways.It is clear that stress, including stress in early life, can alter microbiota composition and this can have marked consequences on physiology in adulthood.Studies in germ-free animals and in animals exposed to pathogenic bacterial infections, probiotic bacteria or antibiotic drugs suggest a role for the gut microbiota in the regulation of anxiety, mood, cognition and pain.Although not as conceptually or empirically developed, the gut microbiota has also been implicated in obesity, autism and multiple sclerosis.Mechanisms as to how the microbiota are affecting gut–brain signalling are only now being unravelled. These mechanisms may include alterations in microbial composition, immune activation, vagus nerve signalling, alterations in tryptophan metabolism, production of specific microbial neuroactive metabolites and bacterial cell wall sugars.Harnessing such mechanisms may pave the way for microbial-based therapeutics for various CNS disorders.