Most of the CNS neurons that regulate circulation and respiration reside in regions of the brain characterized by extreme cellular heterogeneity (nucleus of the solitary tract, reticular formation, parabrachial nuclei, periaqueductal gray matter, hypothalamus, etc.). The chemical neuroanatomy of these regions is correspondingly complex and teasing out specific circuits in their midst remains a problem that is usually very difficult if not impossible to solve by conventional tract-tracing methods, Fos methodology or electrophysiology in slices. In addition, identifying the type of amino acid or peptide transmitter used by electrophysiologically recorded neurons has been until recently an especially difficult task either for lack of a specific marker or because such markers (many peptides for example) are exported to synaptic terminals and thus undetectable in neuronal cell bodies. In this review, we describe a general purpose method that solves many of these problems. The approach combines juxtacellular labeling in vivo with the histological identification of mRNAs that provide definitive neurochemical phenotypic identification (e.g. vesicular glutamate transporter 1 or 2, glutamic acid decarboxylase). The results obtained with this method are discussed in the general context of amino acid transmission in brainstem cardiorespiratory pathways. The presence of markers of amino acid transmission in specific aminergic pre-sympathetic neurons is especially emphasized as is the extensive co-localization of markers of GABAergic and glycinergic transmission in the brainstem reticular formation.