The distribution of hypothalamic neurons expressing the peptides melanin-concentrating hormone (MCH; 'MCH neurons') or hypocretin/orexin (H/O; 'H/O neurons') was assessed with immunocytochemistry in male rats at high spatial resolution. Data were plotted on a rat brain atlas that includes a recently revised parcellation scheme for the lateral hypothalamic zone. Quantitative analysis revealed approximately three times more MCH neurons than H/O neurons in the hypothalamus, and approximately twice as many within the parcellations of the lateral hypothalamic area (LHA). The LHA contained 60% of MCH neurons and 81% of H/O neurons, and the same five LHA regions contained the vast majority of MCH (87%) or H/O (93%) neurons present within the LHA: namely the LHA dorsal region (LHAd: 31% of H/O; 38% of MCH), suprafornical region (LHAs: 28% of H/O; 11% of MCH), ventral region medial zone (LHAvm: 15% of H/O; 16% of MCH), juxtadorsomedial region (LHAjd: 14% of H/O and MCH) and magnocellular nucleus (LHAm: 5% of H/O; 7% of MCH). The zona incerta (ZI) contained 18% of MCH neurons. A high co-abundance of MCH and H/O neurons outside of the LHA was present in the posterior hypothalamic nucleus (PH: 11% of H/O; 9% of MCH). Morphological analysis revealed MCH and H/O neurons as typically tri-polar with irregularly shaped somata. These data provide a quantitative analysis of neurons expressing either MCH or H/O peptides within the rat hypothalamus, and they clarify differences in the distribution pattern for different subsets of these neuron types, especially within the LHA.