Irreversible genetic alterations underlying human diseases have been widely studied to date. However, it is evident that the potentially reversible epigenetic dysregulations may also have an important role in the disease origin. The studies of epigenetic mechanisms underlying disease onset, progression and pathogenesis have been performed in various human disorders. The epigenetic approaches may reveal useful markers for disease diagnostics, classification and prognostics as well as for progressive pharmacological treatment. This review summarizes the studies of epigenetic dysregulations including aberrant methylation, histone modifications and miRNA alterations in cancer as well as the studies of methylation changes and aberrant histone modifications in neurodegenerative, autoimmune, cardiovascular and other diseases. The imprinting disorders together with the emerging role of epigenetics in nutritional genomics, environment-organism interaction studies and in some other fields are also mentioned.