This article gives an overview of the ethical issues in nutrigenomics research and personalized nutrition. The principles of research ethics, i.e., autonomy, beneficence, nonmalfeasance, and justice, are challenged by rapidly growing cross-border research activities utilizing existing and upcoming biobanks for studies of the interaction of genes with diet on risk of common diseases. We highlight the ethical issues, some unresolved, in international collaborative projects of which researchers should be aware. Personalized nutrition (tailoring diet on the basis of genotype) is one possible application of nutrigenomics research. However, until the scientific evidence concerning diet-gene interactions is much more robust, the provision of personalized dietary advice on the basis of specific genotype remains questionable. From the ethical and social perspective, nutrigenomics offers significant opportunities to improve public health by enhancing understanding of the mechanisms through which diet can be used to reduce the risk of common polygenic diseases.