There is now compelling evidence, coming both from animal and human studies that an early exposure to undernutrition is frequently associated with low birth weight and programs HPA axis alterations throughout the lifespan. Although animal models have reported conflicting findings arising from differences in experimental paradigms and species, they have clearly demonstrated that such programming not only affects the brain but also the pituitary corticotrophs and the adrenal cortex. In fetuses, maternal undernutrition reduces HPA axis function and implicates a reduction of placental 11beta-HSD2 activity and a greater transplacental transfer of glucocorticoids (GRs). In young adults, usually only fine HPA axis alterations were observed, whereas in older ones, maternal undernutrition was frequently associated with chronic hyperactivity of this neuroendocrine axis. In humans, evidence of HPA axis dysregulation in people who were small at birth has recently emerged. Thus, we suggest that such alterations in adults may be implicated in the aetiology of several disorders related to the metabolic syndrome as well as to immune or inflammatory diseases. To reverse such programming, recent experimental reports have shown that postnatal environmental interventions, dietary modifications and the use of agents modulating the epigenomic state could partly restore physiological functions and thus open new therapeutic strategies.