Many environmental factors, including chemicals in cigarette smoke, have deleterious effects on human health. Epidemiological studies have repeatedly confirmed that prenatal exposure to maternal smoking is associated not only with complications of pregnancy, foetal growth retardation and disturbed development, but also with an increased risk of serious diseases manifested during childhood and adulthood. The possible pathways of aberrant foetal programming are the interactions of genes and environmental factors through epigenetic mechanisms. Although these scientific problems are just beginning to be understood, some models of altered epigenetic regulations were described: DNA methylation, non-coding RNA(ncRNA)-mediated gene regulation and histone modification. Our contemporaneous knowledge has confirmed that both active smoking and in utero exposure to cigarette smoke can induce changes in all studied epigenetic pathways, and even can be transmitted to future generations through the male germ line.