Intestines act as not only a digestive and absorption tissue of food but also as the largest immunological organ by containing various numbers and kinds of immunocompetent cells. Accumulating evidence indicates that that the functions of intestinal immunity are affected by gut environments such as dietary materials and commensal bacteria, which is tightly related to the development of immune diseases (e.g., allergy and inflammation) at various tissues. Recent technological advancements in the metabolome analysis, metagenomic analysis of commensal bacteria, and bio-informatics technology allow us to understand tripartite interaction between diets, commensal bacteria, and host immunity, leading to the establishment of new concept of drug design. In this talk, I will introduce our studies related to lipids derived from diets and commensal bacteria-mediated immune regulation and the application to the development of anti-allergic and anti-inflammatory medicines.