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The term epigenetics refers to heritable changes in gene expression that are not caused by modifications in DNA sequence. Epigenetic changes are DNA methylation, histone modifications, nucleosome positioning, and non-coding RNA (including microRNA) mediated modifications. Epigenetic mechanisms are involved in malignant diseases, imprinting defects, and some hereditary diseases. Recent research explained the role of epigenetic disorders in infections, autoimmune, neurodegenerative and bone diseases, as well as in psoriasis, endometriosis, and polycystic ovary syndrome. Epigenetic modifications have a potential clinical application as diagnostic and prognostic biomarkers, and also as therapeutic targets in oncology, endocrinology, cardiology, and neuropsychiatry. Stress, anxiety, depression, emotions and many other psychological factors may affect epigenetic mechanisms. Influence of preconception parental stress exposure transmits to the next generation through epigenetic changes, as direct results of prenatal and postnatal environmental factors. Epigenetic changes identify environmental factors which affect health and cause disease onset. Milk is the sophisticated system of communication between mother and infant, operating via epigenetic mechanisms. Lifelong consumption of bovine milk causes epigenetic disorders. Recent studies provide important information about the role of bioactive dietary nutrients which modify epigenome in malignancy prevention and therapy. Any interruption in the balance of intestinal microbiota initiates aberrant epigenetic modifications. Epigenetic patterns act as the “molecular watches” and they play the central role in the establishment of biological rhythms. Epigenetic mechanisms can determine the result of assisted reproductive technology and genetic engineering. The extensive research about the association of epigenetics and pharmacology led to the development of pharmacoepigenetics. All these results emphasize the importance of further research which will take into account all factors that may affect epigenetic mechanisms. [Project of the Serbian Ministry of Education, Science and Technological Development, Grant no. ON-173014]