In recent years investigations of inflammatory bowel disease (IBD) have advanced rapidly with regard to the relationship between the host immune response and gut microbiota. Patients with IBD have been shown to have an abnormal composition of gut microbiota and host immune dysregulation. Abnormal components of gut microbiota, to which the host mounts aberrant immune responses in genetically vulnerable individuals, appear to play a critical role in the pathogenesis of IBD. Therefore, inappropriate innate and adaptive host immune responses to abnormal components of gut microbiota and their products form the basis of IBD pathogenesis. Modern molecular genetic methods should be utilized to help to illuminate the pathogenetic mechanism of IBD and to develop personalized therapeutic strategies for this disease.