There is increasing evidence that the composition of the resident bacteria within the gastrointestinal tract can influence the brain and behavior, particularly with respect to cognitive function. Cognitive function encompasses the life-long process of learning, both long- and short-term processes. Cognition was originally thought to be exclusively regulated by the central nervous system, with long-term potentiation and neurogenesis contributing to the creation and storage of memories, but now other systems, including, for example, the immune system and the intestinal microbiome may also be involved. Cognitive impairment has been identified in numerous disease states, both gastrointestinal and extraintestinal in nature, many of which have also been characterized as having a role for dysbiosis in disease pathogenesis. This includes, but is not limited to, inflammatory bowel diseases, irritable bowel syndrome, type 1 diabetes, obesity, major depressive disorder, and autism spectrum disorder. The role of cognition and the microbiome will be discussed in this chapter for all these diseases, as well as evidence for a role in maintaining overall human health and well being. Finally, evidence for a role for probiotics in beneficially modulating the microbiota and leading to improved cognition will be discussed.