Accumulating evidence indicates many brain functions are mediated by epigenetic regulation of neural genes, and their dysregulations result in neuronal disorders. Experiences such as learning and recall, and physical exercise induce neuronal activation through epigenetic modifications and by changing noncoding RNA profiles. Animal models, brain samples from patients, and the development of diverse analytical methods have broadened our understanding of epigenetic regulation in the brain. Diverse and specific epigenetic changes are being suggested to correlate with neuronal development, learning and memory, aging and age-related neuronal diseases. Although there are some discrepancies among the results, a careful comparison of the data, including methods, regions and conditions examined, would clarify the problems confronted in understanding epigenetic regulation in the brain.