Studies on global human genomic variation have shown important population-based differences in allele frequencies of common single-nucleotide polymorphisms (SNPs) that influence the expression of genes related to nutrition and, secondarily, chronic disease. Some SNP sites have known functions or associations with diseases or other phenotype characteristics, including nutritional deficiencies and metabolism dietary components. There are many components of human diets that, when combined with the impact of diverse genetics on the metabolism of certain nutrients, have the capacity to give rise to harmful diet-gene interactions. This situation has the potential capacity to modify molecular phenotypes and clinical phenotypes, including human disease. Obesity, diabetes mellitus, chronobiology, osteoporosis, cancer, and many other diseases are fields of potential investigation in this topic area. This Special Issue will include manuscripts that focus on the complex relationship between gene polymorphisms and nutrition across all physiological and chronic diseases.