Food allergy is a substantial cause of distress in humans. Several biotechnological techniques can be applied to reduce the antigenicity of food proteins to produce for instance hypoallergenic infant formulas. Biotechnological techniques synthesizing new proteins or new biological varieties for applications in food are also available. For such biotechnologically for derived protein products (novel foods), allergenicity may also pose a major concern. For safety reasons, it is of importance to evaluate the residual antigenicity of modified protein products, to screen for possible cross-reactivity to prevent reactions in previously sensitized individuals, and to test for sensitizing properties of new and/or modified protein products. Besides physico-chemical and immunochemical analyses, several in vitro and in vivo bioassays may be applied in studying the antigenic or allergenic properties of (new or modified) food proteins. In this paper, an overview of several available assays and new developments for determining the antigenic or allergenic properties of dietary proteins, as well as their possible applications and limitations is presented. Special attention is paid to the role of the gastro-intestinal tract physiology in food allergy and in the evaluation of the allergenic potential of food proteins and to the possible applications of animal models in food allergy research and in the evaluation of the allergenicity of food proteins.