Traditional studies on the combined effects of genetics and the environment on individual variation in disease susceptibility primarily focus on single nucleotide polymorphisms that influence toxicant uptake and metabolism. A growing body of evidence, however, suggests that epigenetic mechanisms of gene regulation, such as DNA methylation and chromatin modification, are also influenced by the environment, and play an important role in the fetal basis of adult disease susceptibility. Studying the influence of early environmental exposures on metastable epialleles and imprinted genes offers insight into the mechanisms affecting the fetal epigenome and subsequent adult disease susceptibility. In this review, we introduce the reader to the field of environmental epigenomics, provide information on the important epigenetic control mechanisms and epigenetic phenomena in mammals, and summarize the current body of literature on nutritional and environmental influences affecting the epigenome.