Not only genetic but also epigenetic mechanisms regulate gene expression, cellular differentiation and development processes. Additionally, "environmental epigenetics" studies the interaction between the environment and the epigenome, and its potential role in the regulation of gene activity. Several studies have shown that the impact of environmental exposures on the epigenome takes on more importance during early fertilization and embryonic development, given that during these periods epigenetic reprogramming occurs and the new epigenetic profile of the offspring is established. Epigenetic alterations in the germline are especially relevant since they can be transmitted trans-generationally and could be associated with a wide range of diseases including several reproductive disorders. In this chapter we review some epigenetic mechanisms, focusing mainly on DNA methylation and histone modifications, which are related to reproductive aspects, and we discuss the controversies in the literature surrounding how environmental conditions, such as exposure to toxic substances or treatment with assisted reproductive techniques (ART), may be involved in epigenetic alterations that affect reproductive success.