Gut is composed of more bacterial organisms than the number of eukaryotic cells. Gut microbiota plays a vital role in the post natal maturation of the immune system, digestion and absorption of macromolecules, protection of gut from pathogens and behavioral development. It triggers the innate immunity causing the maturation of gut associated lymphoid tissue, and acquired immunity by stimulating the local and systemic immune responses. Persistent stimulation of the immune system by gut microbiota leads to low grade physiological inflammation, for defence against pathogens. This chapter covers the gut microbiota and mood disorders, gut microbiota and stress response via HPA axis, gut microbiota and autism, association between gut microbiota, myelination and neuropsychiatric disorders, gut microbiota and parkinsonism, influence of maternal microbiota on the fetus and its effect on the brain development, gut microbiota and hologenomic theory of evolution, gut microbiota in the pathogenesis of multiple sclerosis, and role of nervous system in gut infection.