A variety of events during fetal and neonatal life can influence body composition, circulating hormones, expression of brain transmitters and brain function in later life, but it is less clear how the initial adverse events are linked mechanistically to these outcomes. Whereas changes in DNA sequence, for example through mutation, can have profound effects on key outcomes such as body adiposity, an additional level of complexity is provided by epigenetic regulation. Epigenetic modification affects the way the genetic code is interpreted, and may be as important as the sequence itself. Epigenetic ‘marking’ of the genome can be influenced by factors such as diet and lifestyle and has been implicated in long-term health. Both heritable and non-heritable processes contribute to brain development, and epigenetic processes are likely to be particularly prevalent in the brain, given its anatomical and physiological complexity. The hypothalamus and brainstem, for example, express a high proportion of the known imprinted genes. That these ‘hotspots’ are associated with energy balance is clearly of interest in the context of perinatal programming of maladapted body phenotype and metabolic status. Nutritionally acquired epigenetic modification during brain development has been demonstrated in the hypothalamus and in the reward circuitry in higher brain circuits.