Genetic research has focused on identifying linkages between polymorphisms and phenotypic traits to explain variations in complex biologies. However, the magnitude of these linkages has not been particularly high. Conversely, the ability of developmental plasticity to generate biological variation from one genotype is well understood, while interest has emerged in the clinical significance of epigenetic processes, particularly those influenced by the external environment. Environmental cues in early development may induce responses that provide adaptive advantage later in life. The benefit of such responses depends on the fidelity of the prediction of the future environment. Life history and physiological changes mediated through epigenetic processes then follow, determining the later phenotype. Developmental mismatch, leading to disease, can arise from discordance between the fetal environment, which is relatively constant across generations, and the postnatal nutritional environment, which can change drastically within and between generations. Metabolic disorders represent the outcome of an individual living in an energetically inappropriate environment. Experimental and clinical evidence suggests that individual capacity to live in a given energetic environment is influenced by developmental factors acting through epigenetic mechanisms. Epigenetic biomarkers may be able to identify a risk of developmental mismatch and thus offer the opportunity for nutritional or other intervention.