The gastrointestinal system is not only the primary pathway for the entry of xenobiotics into the body, but also a major metabolic and immunologic organ. Each of these three functions is essential to the body's correct function that, if disrupted, can lead to at best great discomfort and impaired function. The interactions of the components of the gastrointestinal tract are complex, and because the functions are interactive, the detecting and characterization of adverse effects on the functions, and the determination of dose–response relationships for these effects can be equally complex. In this chapter, the structure, function and interaction of the gastrointestinal system is outlined, together with details of how adverse effects can be detected and characterized.