Recent studies have demonstrated a clear association between changes in the microbiota and cognitive behavior. Intestinal dysbiosis, as modeled using GF mice (containing no microbiota), bacterial infection with an enteric pathogen, and administration of probiotics, can modulate cognitive behavior including learning and memory. This chapter will highlight recent findings in both human and animal studies indicating how changes in the composition and diversity of the microbiota can impact behavior and brain physiology in both disease states and in health. Cognitive behavior can not only be affected in cases of intestinal disease, but also manifests changes in extra-intestinal disease conditions.