We measured putrescine levels in minute sites of single rat brains using a sensitive, specific assay involving gas chromatography-mass spectrometry. The putrescine level was measured in 20 sites of single rat brains: three sites in the cerebral cortex, six sites in the hypothalamus, three sites in the basal ganglia, three sites in the thalamus, three sites in the limbic system, and two sites in the cerebellum. The level of putrescine was very high in the hypothalamus, high in the basal ganglia and limbic system, and low in the thalamus, cerebellum, and two of the three sites in the cerebral cortex. The highest levels were in the anterior hypothalamic area and the lateral hypothalamic area, and the lowest levels were in the vermis and the lobe of the cerebellum.