Nutrigenomics represents a shift of nutrition research from epidemiology and physiology to molecular biology and genetics. Nutrigenomics seeks to understand nutrition influences on homeostasis, the mechanism of genetic predispositions for diseases, to identify the genes influencing risk of diet related diseases. This review presents some in vitro models applicable in nutrigenomic studies, and discuses the use of animal models, their advantages and limitations and relevance for human situation. In vitro and in vivo models are suitable for performance of DNA microarrays, proteomic and transcriptomic analyses. In vitro models (intracellular organelles and suborganellar compartments, cell cultures, or tissue samples/cultures) give insight in metabolic pathways and responses to test stimuli on cellular and molecular levels. Animal models allow evaluation of the biological significance of the effects recorded in vitro and testing of the hypothesis on how a specific factor affects specific species under specific circumstances. Therefore, the evaluation of the data in relation to human organism should be done carefully, considering the species differences. The use of in vitro and in vivo models is likely to continue as the effects of nutrition on health and disease cannot be fully explained without understanding of nutrients action at nuclear level and their role in the intra- and intercellular signal transduction. Through advances in cell and molecular biology (including genomic and proteomic), the use of these models should become more predictively accurate. However, this predictive value relies on an underpinning knowledge of the advantages and limitations of the model in nutrigenomic research as in other fields of biomedical research.