The number of offspring conceived by assisted reproductive technology (ART) has reached over 5 million. As the primary means for treating infertility, the health of offspring produced by ART has been a long concern. Both procedures of ART and factors underlying infertility can lead to epigenetic changes which can cause certain diseases. This paper has reviewed diseases noted among offspring conceived by ART, which include imprinting disorders, metabolic syndromes and cancers. We also tried to explore the pathogenesis of such diseases from an epigenetic perspective, which may help with evaluation the influence of ART on the offspring and its safety for application.