A fundamental question important to the understanding of the neurochemical organization of the central nervous system focuses on the relationships between the differential phenotypic expression of multiple neurotransmitter markers in individual neuronal populations and the factors that regulate their expression. The first approach in studying this phenomenon is the determination of specific relationships between neurochemically distinct neuronal subpopulations and their efferent targets. The pontine nucleus locus coeruleus (LC) provides a useful model for addressing this question since the projections of LC neurons are topographically organized and several neuropeptides are expressed along with noradrenergic markers in subsets of these neurons. In these studies, we have focused on defining the efferent targets of LC neurons that contain neuropeptide tyrosine (NPY)-like immunoreactivity. This has been accomplished by injecting the retrograde fluorescent tracer fluorogold into specific cortical and hippocampal targets in adult rats and identifying the proportion of retrogradely labeled LC neurons that are positive for NPY-like immunoreactivity. In agreement with other investigators, no preferential cortical projections of NPY-positive LC neurons were observed. However, when fluorogold injections included or were limited to the entorhinal cortex, a discrete cluster of round or ovoid neurons in the dorsomedial portion of the LC approximately 9.8 mm posterior to bregma were found to contain NPY-like immunoreactivity. This observation demonstrates that some topographic organization of NPY-containing LC neurons does exist. In fact, these data indicate that morphologic and topographic organization exists even within neurochemically distinct subsets of neuronal populations.