Cocaine abuse is associated with autonomic dysregulation, such as altered blood pressure and heart rate. Both central and peripheral mechanisms have been implicated in mediating these changes, however, to date, no study has examined functional changes in activity within central autonomic-associated brain regions in response to cocaine in non-human primates. The aim of the present study was to measure local cerebral glucose utilization, in selected autonomic brain regions, in rhesus monkeys that had self-administered cocaine (0.3 mg/kg/infusion) for 5 days (initial) or 100 days (chronic). Measurements were compared with control monkeys, in which responding was maintained by food reinforcement. In general, decreased rates of glucose utilization were observed in targeted areas following both 5 and 100 days of cocaine self-administration compared to control values. However, after initial stages of cocaine exposure, significant reductions in the forebrain were restricted to the bed nucleus of stria terminalis and in the brainstem to the nucleus tractus solitarius and dorsomotor nucleus of the vagus nerve. The pattern of significantly altered functional activity induced by chronic 100-day cocaine self-administration extended within the forebrain to include the paraventricular hypothalamic nucleus, and in the brainstem to include additional autonomic-related nuclei, the nucleus ambiguus and locus coeruleus. These results suggest that even at the initial stages of cocaine self-administration, functional changes in activity occur in autonomic and reward-related brain regions. These alterations progress with prolonged cocaine exposure, and therefore may be involved in mediating changes in central autonomic control and the neuroadaptations reported to result from chronic drug abuse.