Independent of the cause and location, inflammation - even when minimal - has clear effects on gastrointestinal morphology and function. These result in altered digestion, absorption and barrier function. There is evidence of reduced villus height and crypt depth, increased permeability, as well as altered sugar and peptide absorption in the small intestine after induction of inflammation in experimental models, which is supported by some clinical data. Identification of inflammatory factors which may promote the process of gastrointestinal dysfunction as well as clinical research to verify experimental observations of inflammatory modulation of gastrointestinal function are required. Moreover, nutritional strategies to support functional restitution are needed.