Melanin-concentrating hormone (MCH) is a potent orexigenic and sleep-promoting neuropeptide in mammals produced predominately by hypothalamic neurons which project to a wide variety of brain areas. Several MCH producing neurons contain MCH as the only neuropeptide, while others comprise cocaine- and amphetamine regulated transcript (CART) as well. The intrahypothalamic localization and the projection pattern of these two subpopulations are distinct. To provide structural grounding to understand the mechanism of action of MCH neurons we show here the subcellular localization of the neuropeptides in the two subpopulations within the hypothalamus of healthy young male mice by applying single and double immunofluorescence labelling.; Thick, prominent MCH immunopositive reticulation and fine discrete granules are detected within the perikarya of both CART positive and CART-free MCH neurons. Typically, one or more immunoreactive processes emanate from the perikarya. The bulk of CART immunoreactivity is also centrally positioned, surrounded by sparse immunoreactive granules within the perikarya and in the processes. In double immunopositive neurons, the two neuropeptides seem to colocalize in the heavily labelled central area, while the immunopositive granules in the cell body periphery and in the processes apparently contain either MCH or CART. This spatial arrangement suggests that MCH and CART, after being synthetized and processed in the endoplasmic reticulum/Golgi complex, are sorted into separate dense core vesicles, which then enter into the cell processes. This mechanism allows for both concerted and independent regulation of the transport and release of MCH and CART.