Spermatogenesis is a highly complex process involving mitotic cell division, meiosis and the process of spermiogenesis, during which unique and extensive chromatin and epigenetic modifications are remodeled to bring about specific epigenetic profiles for spermatozoa. Recent studies have shown that epigenetic modifications in mature spermatozoon play an important role in the developing embryo and its alterations in epigenetic patterns may increase the risk for fertilization failure, dysfunction of embryogenesis, preterm birth, low birthweight, congenital anomalies, perinatal mortality, and several other pregnancy-related complications seen at a higher frequency in babies conceived by in vitro fertilization (IVF). In this review, we assess the significance of epigenetic modifications (DNA methylation, histone retention and modification, RNAs and protamine) in mature spermatozoon and its potential role in embryonic development, and elucidate the relationship between altered epigenetic profile and associated diseases, providing basic information for preventing and treating male infertility, evaluating the epigenetic quality of sperm and reducing the risk of epigenetic diseases with babies conceived by assisted reproductive technology (ART).