This review discusses the growing body of evidence that both PAE and developmental stress exposure affect an individual’s cognitive development and risk for psychopathology in part through changes to the epigenome. The primary focus of this review is on animal models of PAE or gestational or postnatal stress as most epigenetic research has utilized these models. Where appropriate, the translational relevance of animal data is discussed. Areas where the effects of developmental alcohol and stress intersect will be discussed as well. These areas of overlap include discussion of epigenetic modification of genes involved in neural development and hypothalamic–pituitary–adrenal (HPA) axis regulation, molecules involved in the regulation of epigenetic marks, and miRNA expression. In addition, we discuss important areas for further research, including multigenerational effects of alcohol and stress as a way in which teratogen exposure could impact the health and well-being of several generations, and possible pharmacological, nutritional, and behavioral interventions to rescue negative outcomes of developmental alcohol or stress exposure, specifically in relation to their effect on the epigenome.