Recently, a list of clinical, physiopathological, and epidemiological studies has underlined the detrimental or beneficial role of nutritional factors in some chronic diseases such as obesity, type 2 diabetes, cardiovascular disease, and cancer. It has been described that lifestyle, environmental conditions, and nutritional compounds influence gene expression. In the last instance, it has been demonstrated that bioactive nutrimental components are important signal molecules that carry information from the external environment and could affect in biological terms, processes related to gene expression. Bioactive nutriments can work in different ways: regulating the chromatin structure or factors that directly regulate the activity of nuclear receptors. The relevance of the changes in the chromatin structure has been demonstrated by the fact that many chronic diseases and metabolic disorders are related with changes in DNA methylation patterns. For this reason, recently, the bioactive food nutriments have been investigated to characterize the molecular mechanism involved in changes of the chromatin structure, such as acetylation and methylation, and their potential benefit on chronic diseases. The dietary compounds intake involved in the regulation of epigenetic modifications can provide significant health effects and may prevent various pathological processes involved in the development of cancer and other serious diseases.