The gastrointestinal immune system is a major component of the mucosal barrier to foreign antigens including microbial and dietary antigens. Under normal circumstances, the mucosal immune system employs tightly regulated dynamic mucosal intra- and internets for the maintenance of an appropriate immunological balance between the host and gut environments. For example, mucosally induced tolerance is usually induced against enteric commensal bacterial and/or dietery antigens. However, in some cases, the break down of these tightly regulated mucosal immune responses led to hyper-responsiveness against these gut environmental antigens. To this end, numerous disorders could evoke in the gastrointestinal tissues, such as inflammatory bowel disease (IBD) and allergic gastroenteropathy. Recently, many studies have described possible molecular and cellular mechanisms of those dysfunctions in the gastrointestinal tissues. In this review, we have briefly summarized some of the current interesting and exciting findings for gastrointestinal diseases, especially IBD and intestinal allergic diseases from our group, which can be applied for the development of new mucosal immune therapy.