The retrotrapezoid nucleus (RTN) contains noncholinergic noncatecholaminergic glutamatergic neurons that express the transcription factor Phox2b (chemically coded or "cc" RTN neurons). These cells regulate breathing and may be central chemoreceptors. Here we explore their ultrastructure and their acid sensitivity by using two novel BAC eGFP-Phox2b transgenic mice (B/G, GENSAT JX99) in which, respectively, 36% and 100% of the cc RTN neurons express the transgene in complete or partial anatomical isolation from other populations of eGFP neurons. All but one of the eGFP-labeled RTN neurons recorded in these mice were acid activated in slices. These cells contained VGLUT2 mRNA, and 50% contained preprogalanin mRNA (determined by single-cell PCR in the B/G mouse). Two neuronal subgroups were revealed, which differed in discharge rate at pH 7.3 (type I approximately 2; type II approximately 4 Hz) and the degree of alkalization that silenced the cells (type I 7.4-7.6, type II 7.8-8.0). Medial to the RTN, C1 neurons recorded in a tyrosine hydroxylase-GFP mouse were pH insensitive between pH 6.9 and pH 7.5. Ultrastructural studies demonstrated that eGFP-labeled RTN neurons were surrounded by numerous capillaries and were often in direct contact with glial cells, pericytes, and the basement membrane of capillaries. Terminals contacting large proximal eGFP dendrites formed mainly symmetric, likely inhibitory, synapses. Terminals on more distal eGFP dendrites formed preferentially asymmetric, presumably excitatory, synapses. In sum, C1 cells are pH insensitive, whereas cc RTN neurons are uniformly acid sensitive. The RTN neurons receive inhibitory and excitatory synaptic inputs and may have unfettered biochemical interactions with glial cells and the local microvasculature.