We utilized cytochrome oxidase (CO) as a marker of neuronal functional activity to examine metabolic changes in brain stem respiratory nuclei of rats from newborn to 21 day of age. The pre-Bötzinger complex (PBC), upper airway motoneurons of nucleus ambiguus (NA(UAM)), ventrolateral nucleus of solitary tract (NTS(VL)), and medial and lateral parabrachial nuclei (PB(M) and PB(L), respectively) were examined at postnatal days (P) 0, 1, 2, 3, 4, 5, 7, 14, and 21. CO histochemistry was performed, and the intensity of CO reaction product was quantitatively analyzed by optical densitometry. In addition, CO histochemistry was combined with neurokinin-1 receptor (NK1R) immunogold-silver staining to doubly label neurons of PBC in P14 animals. The results showed that levels of CO activity generally increased with age in all of the nuclei examined. However, a significant decrease was found in NA(UAM) at P3 (P < 0.01), and a distinct plateau of CO activity was noted at P3 in PBC and at P3 and P4 in NTS(VL), PB(M), and PB(L). Of the neurons examined in PBC, 83% were doubly labeled with CO and NK1R. Of these, CO activity was high in 33.9%, moderate in 27.3%, and light in 38.8% of neurons, suggesting different energy demands in these metabolic groups that may be related to their physiological or synaptic properties. The transient decrease or plateau in CO activity at P3 and P4 implies a period of synaptic adjustment or reorganization during development, when there may be decreased excitatory synaptic drive or increased inhibitory synaptic drive, or both, in these brain stem respiratory nuclei. The adjustment, in turn, may render the system less responsive to respiratory insults. This may bear some relevance to our understanding of pathological events during postnatal development, such as occurs in sudden infant death syndrome.