The understanding of the role of nutrients on DNA stability, repair and on the different gene expression processes recently became more prominent in nutritional science. Nutrients and the genomics interact at two levels. Nutrients can induce gene expression thereby altering individual phenotype. Conversely single nucleotide polymorphisms, in a range of genes important in inflammation and lipid metabolism, alter the bioactivity of important metabolic pathways and mediators and influence the ability of nutrients to interact with them. The study on single effects of nutrients on the individual's phenotype as well as the serial analyses of gene expression patterns in response to specific nutrients will help us to understand how metabolic homeostasis is maintained. Considering that there is wide variation in the ability of nutritional factors to modulate the expression of detrimental or protective proteins at an individual level, the concept of diet-medication could be developed in the light of a better understanding of nutrient-gene interactions. In this way, 'good responders' and 'poor responders' to diet therapy can be identified. Furthermore, as several vitamins participate in DNA protection and genomic stabilisation, diet-linked therapies could become part of cancer prevention and other treatments with relevant consequences for human health.