The retrotrapezoid nucleus (RTN) provides a source of tonic drive to respiratory neurons and is one of many sites for central chemoreception. Here we evaluate in the rat the local neuronal cytoarchitecture in the RTN histologically 2-4 h after neurobiotin injection and the afferent connections to the RTN 24 h after injection. Our neurobiotin injections often overlapped the RTN and the adjacent neurons of the parapyramidal region, so we group these two regions together in this study. The RTN is made up of small and medium sized neurons and has a low neuronal density compared to other nuclei. The organization of the RTN is reticular in nature and there are prominent small neurons at the ventral medullary border. Adjacent to the pyramids there are medium sized neurons with connections to the raphé pallidus. Major afferent connections include the regions of the dorsal and ventral respiratory groups, the medullary raphé, the contralateral parapyramidal and RTN regions, portions of the nucleus paragigantocellularis lateralis, and portions of the reticular fields. Other sources of input include the Kölliker-fuse nucleus, subceruleus, A5 region, and the paralemniscal zone.