Insulin and amylin are cosecreted by pancreatic B cells and have receptors within the central nervous system (CNS), where they exert multiple effects. Although these peptides are not produced in the CNS, their ability to cross the blood-brain barrier (BBB) explains their presence there. We used multiple-time regression analysis to measure, in mice, the unidirectional influx constant (Ki) of each of these peptides to compare their rates of transport with each other and in different regions of the brain. The uptake of amylin by whole brain and by the cerebellum, midbrain, frontal cortex, parietal cortex, and occipital cortex was greater than that for insulin. For amylin, the areas of highest uptake were the pons-medulla and the cerebellum, and the areas of lowest uptake were the thalamus and midbrain. For insulin, the areas of highest uptake were the pons-medulla and the hypothalamus, whereas three regions (midbrain, thalamus, and occipital cortex) did not have a measurable Ki. The peak percent of injected dose taken up by whole brain was 0.12% for amylin and 0.046% for insulin. These results show that the permeabilities of these two peptides across the BBB differed from each other and among brain regions, suggesting that differential permeability of the BBB for blood-borne peptides could provide a mechanism by which their effects on the CNS are regulated.