The gastrointestinal tract is very complex. It performs numerous functions, centering on the conversion of food to basic nutrients and energy. The many functions of the gastrointestinal tract may be assessed through proven methodology. A number of published assays for the assessment of gastrointestinal functionality are targeted for the human population, but many of these may also be utilized in laboratory animals. There are numerous validated methods, however, that do assess gastrointestinal functionality, and are appropriate for preclinical testing in vivo and in vitro. Gastrointestinal functions include, but are not limited to, transit, absorption, digestion, secretion, microflora, immunity, and viscerosensitivity (abdominal pain). Specific tests and models for functional analyses are also discussed.