Previous studies have described the distribution of melanin-concentrating hormone (MCH) and neuropeptide EI (NEI) in the rat central nervous system (CNS), and revealed this peptidergic system to be primarily localized in neurons within the lateral hypothalamic area (LHA) and zona incerta (ZI). Moreover, an extensive MCH- and NEI-immunoreactive (ir) fiber distribution has been described throughout the CNS, including a dense innervation within the periaqueductal gray matter (PAG). MCH and NEI have become important markers for the LHA, which harbors a variety of neuronal types as well as the medial forebrain bundle, a complex system of fibers which extends rostrocaudally throughout this area. In the present study, the projection patterns of MCH- and NEI-ir fibers within the PAG were characterized using a diamino benzidine immunoperoxidase procedure to localize each of these peptides in normal rat brain sections. MCH- and NEI-ir fibers were seen coursing through all of its subdivisions the entire length of the PAG, with a more condensed number of fibers in the periaqueductal medial zone. The primary origin(s) of these PAG afferents were determined in combined retrograde tracing immunofluorescent studies in which true blue (TB) was injected into various subdivisions of the PAG. TB-filled MCH-ir neurons were identified mainly in the rostral portion of the medial ZI (ZIm) and in the tuberal LHA (LHAt). Studies confirming this MCH-ir projection in which anterograde tracer (Phaseolus vulgaris leucoagglutinin) was injected into various regions in and around the LHA and ZI revealed a distinction in the PAG projections arising from these nuclei. ZIm injections resulted in labeled fibers mainly within the rostral dorsomedial and dorsolateral regions of the PAG, whereas injections in the LHAt revealed an innervation at intermediate and caudal levels in the ventrolateral region. Since the MCH and NEI fiber distribution patterns in the PAG are identical, this would suggest that these peptides are colocalized within the hypothalamus. Sequential immunofluorescent staining for MCH and NEI on tissue from rats who had received TB injections into the PAG confirmed this, and revealed that approximately 15% of all tracer-filled neurons in the LHA and ZI were both MCH- and NEI-ir. In fact, the vast majority of MCH-ir neurons within these regions also colocalize with NEI. Therefore, the MCH/NEI projection patterns within the PAG arise from two major sources: the ZIm which supplies afferents via a medial pathway that enters the PAG dorsally at rostral levels, and a pathway originating in the LHA that enters the PAG ventrally at more caudal levels. The ZIm and LHA are believed to be the primary, if not the only, sources of MCH and NEI projections to the PAG.