1. 5-hydroxytryptamine (5-HT) level was measured in hypothalamus, striatum and the rest of the brain of rats exposed to 1800, 5200 and 7000 m simulated altitudes. 2. Moderate hypobaric hypoxia failed to modify 5-HT level, whereas severe hypoxia reduced the amine level by about 30%. 3. Treatment with a synthesis blocking agent (PCPA) revealed a dual effect of hypoxia on the 5-HT elimination. Increased elimination observed at 1800 m was attributed to the hypoxia-induced stress and the decrease (at 5200 and 7000 m) indicated the predominance of enzymatic inhibition. 4. It was assumed that tryptophan hydroxylase was more sensitive than monoamine oxidase to a high hypobaric hypoxia.