Previously we reported that during protracted morphine abstinence rats show reduced conditioned place preferences (CPP) for food-associated environments, compared to non-dependent subjects. To determine the brain regions involved in this altered reward behavior, we examined neural activation (as indexed by Fos-like proteins) induced by a preference test for a food-associated environment in 5-week morphine-abstinent versus non-dependent animals. The results indicate that elevated Fos expression in the anterior cingulate cortex (Cg) and basolateral amygdala (BLA) correlated positively with preference behavior in all groups. In contrast, Fos expression in stress-associated brain areas, including the ventral lateral bed nucleus of the stria terminalis (VL-BNST), central nucleus of the amygdala (CE), and noradrenergic (A2) neurons in the nucleus tractus solitarius (NTS) was significantly elevated only in morphine-abstinent animals. Furthermore, the number of Fos positive neurons in these areas was found to correlate negatively with food preference in abstinent animals. These results indicate that the altered hedonic processing during protracted morphine withdrawal leading to decreased preference for cues associated with natural rewards may involve heightened activity in stress-related brain areas of the extended amygdala and their medullary noradrenergic inputs.