The effects of hypoxia FiO2 = 0.10 on concentration of biogenic amines in specific brainstem nuclear groups were investigated in 3-and 21-day-old rabbits. The rabbit pups were confined to temperature-controlled water-jacketed chambers and exposed to 6h of 21% O2 or to one of 3 combinations of 21% O2 and 10% O2. These 3 combinations were either intermittent hypoxia, or 4 h of normoxia followed by 2 h constant hypoxia, or 2 h of hypoxia followed by recovery for 4 h in normoxia. Radioenzymatic assays were used to determine the concentration of dopamine, norepinephrine and serotonin in the following brainstem nuclei: substantia nigra, locus coeruleus, dorsal raphe and the nucleus reticularis pontis oralis. Compared with control, hypoxia did not affect dopamine levels at either age. The concentration of norepinephrine was inconsistently affected by hypoxia at either age. In contrast, in the 3-day-old rabbits serotonin was consistently reduced in each of the nuclei. In the 21-day-old rabbits, serotonin was either unchanged or increased following hypoxia. Our results show that hypoxia alters the concentration of serotonin in an age-specific manner. This change in serotonin concentration may reflect altered serotonin metabolism and suggests a possible mechanism by which hypoxia disrupts physiologic homeostasis in newborns.