Identification of two markers of neurons in the pre-Bötzinger complex (pre-BötC), the neurokinin 1 receptor (NK1R) and somatostatin (Sst) peptide, has been of great utility in understanding the essential role of the pre-BötC in breathing. Recently, the transcription factor dbx1 was identified as a critical, but transient, determinant of glutamatergic pre-BötC neurons. Here, to identify additional markers, we constructed and screened a single-cell subtractive cDNA library from pre-BötC inspiratory neurons. We identified the glycoprotein reelin as a potentially useful marker, because it is expressed in distinct populations of pre-BötC and inspiratory bulbospinal ventral respiratory group (ibsVRG) neurons. Reelin ibsVRG neurons were larger (27.1 ± 3.8 μm in diameter) and located more caudally (>12.8 mm caudal to Bregma) than reelin pre-BötC neurons (15.5 ± 2.4 μm in diameter, <12.8 mm rostral to Bregma). Pre-BötC reelin neurons coexpress NK1R and Sst. Reelin neurons were also found in the parahypoglossal and dorsal parafacial regions, pontine respiratory group, and ventromedial medulla. Reelin-deficient (Reeler) mice exhibited impaired respones to hypoxia compared with littermate controls. We suggest that reelin is a useful molecular marker for pre-BötC neurons in adult rodents and may play a functional role in pre-BötC microcircuits. J. Comp. Neurol. 520:606–619, 2012. © 2011 Wiley Periodicals, Inc.