The complex interactions between microbial, genetic, immune, and environmental factors seem to play an important role in the pathogenesis of IBS, IBD and CRC. Lately, post infectious - IBS have gained increasing focus, to the extent that whole pathogenesis of IBS might be attributed to a specific triggering factor of microbiota imbalance. The prevailing theory is that IBD is related to an altered mucosal barrier with a deregulated immune response directed against specific modifications in the normal microbiota leading to the alteration of its equilibrium. The etiology of IBD can therefore be conceptualized as an aberrant immunologic response to a modified component or components of the gut microbiota potentially following an environmental insult. Likewise, CRC development process from normal mucosal surface to adenoma and finally to CRC; is probably related to gut microbiota.