The preconceptional and/or periconceptional periods (before and just after fertilization until the embryo blastocyst stage) are critical for the developmental origins of health and disease. Major epigenetic modifications occur during gametogenesis, fertilization, and the early stages of embryonic development. These modifications can be altered by the environment in vivo, particularly through maternal and/or paternal nutrition, but also in vitro, including during procedures such as assisted reproduction. Female gametes, but also male, are involved as targets of the epigenetic modifications and also as vectors of modified epigenetic marks, leading to long-term effects on the offspring. Physiological and epigenetic effects observed vary depending on fetal gender. Although this review focuses on new developments in epigenomics in the horse, most of the mechanism information was derived from mice, men, and cattle. Indeed, although the long-term impact of equine embryo technologies is yet to be evaluated, data from other species already indicate that the nutritional status of both gamete donors and of the recipient mare should not be overlooked. Finally, as opposed to most other domestic species, and closer to the situation in humans, older horses are used for reproduction, and this may also affect the quality of gametes and subsequently offspring to be born.