The first food products derived from transgenic plants that are resistant to diseases, insects or viruses are now reaching the market and there is growing public concern about problems of allergenicity and toxicological changes in such transgenic food plants. This paper reviews the modifications being carried out, or envisaged, in molecular resistance breeding, and specifically considers the allergenic and toxicological potential of the gene products used. Several protein families that contribute to the defence mechanisms of food plants have members which are allergens or putative allergens and some of these proteins are used in molecular approaches to increase resistance. These include alpha -amylase and trypsin inhibitors, lectins and pathogenesis-related proteins. An assessment procedure to avoid the transfer of such allergens is described. The source of the transgene is of great importance for the application of immunological assays. In addition to putative changes in the allergenic potential, the toxicological implications of classical and molecular resistance breeding are discussed. Several 'self defence' substances made by plants are highly toxic for mammals, including humans. Examples of molecular approaches that could be of toxicological concern are given. The source of the transgene is of no relevance in assessing the toxicological aspects of foods from transgenic plants. Food safety can also be severely influenced by invading pathogens and their metabolic products. This may result in a trade-off situation between 'nature's pesticides' produced by transgenic plants or varieties from traditional breeding programmes, synthetic pesticides and mycotoxins or other poisonous products of pests.