Abnormal epigenetic modifications are common in many diseases (such as tumors, senile and developmental diseases), and can influence the pathogenesis and progression of these diseases. Various studies demonstrated that abnormal epigenetic changes could be used as biomarkers for diagnosis of the disease status and prognosis of disease progression. The reversibility and controllability of epigenetic modifications also offer an opportunity to develop new strategies for the early prevention and treatment of diseases. In this review, we provide a brief overview of the latest discoveries in three areas of epigenetic research, i.e., DNA methylation, histone modifications and non-coding RNAs, and their potential applications in early diagnosis and treatment of tumors, senile and developmental diseases. We hope to provide some insights and references in developing strategies for the diagnosis and treatment of these diseases.