Using an established experimental paradigm, feed restriction during the last week of lactation in primiparous sows reduces embryonic growth and development and produces female-specific embryonic mortality by Day 30 of gestation. Because this gender-specific loss of embryos at Day 30 was associated with changes in the variation of markers of epigenetic imprinting, the present study sought to establish the ontogeny of such epigenetic affects. Leucocyte DNA of restrict-fed sows exhibited decreased global methylation during the last week of lactation and during the return to oestrus (P < 0.05), but no associated changes in plasma folate and vitamin B₁₂. Furthermore, no changes in methylation of blastocyst DNA, embryonic sex ratios or development were evident at Day 6 of gestation that would characterise the underlying defects that reduced female embryo survival by Day 30. However, regardless of treatment, embryo recovery rates and synchrony in embryonic development were associated with the stage of development of the recovered embryos (r = 0.68; P < 0.001). The subset of sows classified as bearing litters with superior embryonic development had lower net energy balance over lactation (P < 0.01) and higher ovulation rates (P < 0.005) compared with sows classified as having poorer embryonic development. Collectively, these data suggest that a subset of litters within restrict-fed sows will be most sensitive to the latent epigenetic mechanisms that ultimately trigger gender-specific loss of embryos by Day 30 of gestation, but that these selective mechanisms are not evident by Day 6 of gestation.