Central control of body weight involves coordinated regulation of food intake and energy metabolism. White (WAT) and brown (BAT) adipose tissue represent functionally distinct compartments of lipid storage and fuel consumption, respectively. Both adipose tissues are innervated by the sympathetic nervous system. Tyrosine hydroxylase positive fibers were found in between fat cells. To determine the extent to which the control of different fat compartments is provided by the same pre-autonomic neurons, the central circuit innervating WAT and BAT was compared by dual viral transneuronal tracing using isogenic recombinant strains of the pseudorabies virus. BDL, expressing beta galactosidase was injected to the epididymal WAT and BDG, expressing green fluorescent protein was inoculated into the intrascapular BAT of male rats and virus reporter proteins were revealed by immunocytochemistry. In the spinal cord, BDG infected neurons were found in the intermediolateral and central autonomic nuclei of the upper thoracic segments, while BDL infection appeared in the lower thoracic and lumbar levels. Several brainstem pre-autonomic areas (C1, A5) and the gigantocellular reticular nucleus contained BDG and BDL infected neurons, but relatively few neurons were infected by both viruses. In the dorsal motor nucleus of the vagus, the periaqueductal gray matter, as well as in the dorsomedial, ventromedial, paraventricular hypothalamic nuclei and in the lateral hypothalamic area, anatomically distinct sub-regions were infected by the two recombinant viruses. Following administration of the mixture of BDG and BDL into the WAT, over 70% of the infected neurons contained both recombinant viruses. Our data suggest that neurons involved in the regulation of WAT and BAT coexist in all areas involved in the control of sympathetic outflow, although the relative proportion of these neurons vary across the regions. Double-labeled neurons may represent central command neurons that direct coordinated responses of WAT and BAT to metabolic challenges.