It is well known that the contents of diets affect the healthy condition. In addition, it is also affected by 1,000 kinds of commensal bacteria in the intestinal tract, including interactions with dietary components. Recent development of analytical techniques such as mass spectrometry and next-generation sequencers reveal the molecular relationship among diets, intestinal bacteria and healthy condition. Particularly, gut environmental factors (i.e., diets and commensal bacteria) influence the immune system in the body, subsequently affecting immune responses at various areas in the body, which is involved in various immune diseases as well as other diseases including cardiovascular diseases. In this presentation, I would like to introduce our basic and cohort studies to reveal the interaction between diet and intestinal bacteria as a determinant of immune responses and consequent healthy conditions. I also extend my talk for the development of medicines, functional foods and new medical checkup system.