This review addresses the need to evaluate the biological effects of novel foods, how this can be achieved and the role of animal models in this process. The selection of an appropriate model or combination of approaches is most important, together with an awareness of the shortcomings of that particular method. In mammals the gastrointestinal tract not only acts as the site of absorption of nutrients and non-nutrients, but provides a protective barrier between the environment and the body. As such this interface is exposed to relatively high concentrations of the individual chemicals that are dietary components. It is therefore essential to understand how novel foods can change the structure, growth and function of the gut in particular. Effects may be both beneficial and detrimental and have an impact on the function of other organs in the body. However, due to the wide-ranging implications of this broad topic, the discussion here will focus on events within the gastrointestinal tract, in the context of the evaluation of novel foods.