The brain is the central organ of the body's response to and perception of stress. Both the juvenile and the adult brain show a significant capacity for lasting physiological, structural and behavioral plasticity as a consequence of stress exposure. The hypothesis that epigenetic mechanisms might lie behind the lasting effects of stress upon the brain has proven a fruitful one. In this review, we examine the growing literature showing that stress has a direct impact on epigenetic marks at all life history stages thus far examined and how, in turn, epigenetic mechanisms play a role in altering stress responsiveness, anxiety and brain plasticity across the lifespan and beyond to succeeding generations. In addition, we will examine our own recent findings that stress interacts with the epigenome to regulate the expression of transposable elements in a regionally specific fashion, a finding with significant implications for a portion of the genome which is tenfold larger than that occupied by the genes themselves.