The balance of lipogenesis and lipolysis in fat tissue is regulated both by the interaction of blood born factors and by the autonomic nervous system (ANS). The sympathetic branch stimulates lipolysis, whereas its antagonist, the parasympathetic branch, promotes lipogenesis. Here, by applying two different strains of the retrograde transneuronal tracer Pseudorabies Virus (PRV), we describe a hypothalamic network proximal to the two branches of the ANS. After an injection of PRV-Bartha-80 (PRV-B-80) into the right, sympathetically denervated, retroperitoneal fat pad and a simultaneous injection of PRV-Bartha-GFP (PRV-B-GFP) into the left, parasympathetically denervated, retroperitoneal fat pad we could trace both branches of the ANS up to the hypothalamus within the same animal. We found that pre-autonomic neurons in the suprachiasmatic nucleus (SCN), the paraventricular nucleus of the hypothalamus (PVN) and the lateral hypothalamus (LH) are specialized to project either to sympathetic or to parasympathetic motor neurons. Interestingly, the neurons projecting to these separate autonomic systems share the same brain nuclei. This dual hypothalamic pathway enables hypothalamic centers, such as the biological clock together with temperature and feeding centers, to coordinate metabolic and endocrine functions of adipose tissue.