The ability of living organisms to respond to early nutritional exposures, and to evoke health-related effects in the next generation(s) has led to a growing interest in the “Developmental Origins of Health and Disease” (DOHaD) theory. Whereas maternal contributions are widely examined, effects of the paternal environment are often not considered. Several animal studies and a few epidemiological investigations on parental exposures to malnutrition and obesity indicate that transgenerational inheritance of environmentally induced functional changes of the genome, and related disorders, are driven by epigenetic components. We open the discussion on the existence of epigenetic windows of susceptibility to environmental insults during development of the male germ line. Changes in DNA methylation are viable mechanistic candidates for a non-genetic transfer of parental environmental information, from maturing germ cell to zygote. Inclusion of both, maternal and paternal nutritional factors, in future studies will ultimately improve the understanding of transgenerational epigenetic plasticity and health-related effects in future generations.