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At present, it is vital to examine adverse effects produced on gene expression by negative environmental factors and nutrients. In this study, our aim was to generalize data available in literature on an association between health risks and polymorphisms of genes that participated in xenobiotic detoxification and allergic status, food intolerance included, in adults and children. We also considered influence exerted by various components in diets on gene expression. Available research data indicate that GSTP1 and SOD gene polymorphisms have their effects on a decline in detoxification and antioxidant functions and early development of allergic, occupational and oncological diseases under exposure to harmful chemicals. Micronutrients in diets that can protect from adverse effects produced by chemicals can act not only as substrates but also as detoxification enzyme inducers. Great quantities of biologically active compounds in the Mediterranean diet are assumed to be able to modulate functional activity of certain genes. Such nutrients as polyphenols, flavonoids, catechins, glucosinolates, anthocyanins, stilbenes, carotinoids, polyamines, spermidine and spermine produce anti-genotoxic and anti-carcinogenic effects. Use of combined nutrigenetic and phenotypic data seems a promising trend in effective modeling of a healthy diet. The research data outlined in this review indicate there is solid evidence that health risks can depend on a genotype, phenotype and quality of the environment. These risks also differ depending on a diet. Modeling a healthy diet based on available knowledge on nutritional genetic and nutritional genomics is a promising trend within non-carcinogenic health risk management, including risks of oncological diseases caused by exposure to adverse environmental factors.