Advances in molecular biology greatly contributed, in the past decades, to a deeper understanding of the role of gene function in disease development. Environmental as well as nutritional factors are now well acknowledged to interact with the individual genetic background for the development of several diseases, including cancer, cardiovascular disease, and neurodegenerative diseases. The precise mechanisms of such gene-nutrient interactions, however, are not fully elucidated yet. Many micronutrients and vitamins are crucial in regulating mechanisms of DNA metabolism. Indeed, folate has been most extensively investigated for its unique function as mediator for the transfer of one-carbon moieties for nucleotide synthesis/repair and biological methylation. Cell culture, animal, and human studies, clearly demonstrated that folate deficiency induces disruption of DNA synthesis/repair pathways as well as DNA methylation anomalies. Remarkably, a gene-nutrient interaction between folate status and a polymorphism in methylenetetrahydrofolate reductase gene has been reported to modulate genomic DNA methylation. This observation suggests that the interaction between a nutritional status and a mutant genotype may modulate gene expression through DNA methylation, especially when such polymorphism affects a key enzyme in one-carbon metabolism and limits the methyl supply. DNA methylation, both genome-wide and gene-specific, is of particular interest for the study of aging, cancer, and other pathologic conditions, because it affects gene expression without permanent alterations in the DNA sequence such as mutations or allele deletions. Understanding the patterns of DNA methylation through the interaction with nutrients is a critical issue, not only to provide pathophysiological explanations of a disease state, but also to identify individuals at-risk to conduct targeted diet-based interventions.