We screened transgenic mouse lines with Thy1.2 promoter-induced expression of fluorescent proteins (FPs) for targeting of respiratory neuronal populations in the medulla oblongata. Respiratory neurons were found to be tagged by FPs within the ventral respiratory column (VRC), the pre-Bötzinger complex (preBötC) and the rostral ventral respiratory group (rVRG) interneurons. A subset of neurons in the preBötC, labeled with the enhanced yellow fluorescent protein (EYFP), showed inspiratory activity during whole cell recordings from rhythmic slice preparations. Additionally, a subpopulation of EYFP-labeled preBötC neurons expressed both NK1- and mu-opioid receptors. Furthermore, the spinal trigeminal nucleus, the lateral reticular nucleus (LRT) and the hypoglossal nucleus demonstrated intense EYFP expression whereas other regions of the medulla were devoid of neuronal EYFP labeling (e.g. the nucleus ambiguous). In conclusion, Thy1.2-FP transgenic mice will facilitate the functional analysis of respiratory-related neurons in the medulla and improve the three dimensional analysis of cells contributing to this important neuronal circuit.