The role of transport exchanges of neuroactive solutes across the blood–brain barrier (BBB) is increasingly recognized. To take full advantage of genetically altered mouse models of neurodegenerative disorders for BBB transport studies, we adapted a brain perfusion technique to the mouse. During a carotid brain perfusion with a medium containing sheep red blood cells and mock plasma, the physiological parameters in the arterial inflow, regional cerebral blood flow (¹⁴C -iodoantipyrine autoradiography), ultrastructural integrity of the tissue, barrier to lanthanum, brain water content, energy metabolites and lactate levels remain unchanged. Amyloid-β peptides (Aβ) were iodinated by lactoperoxidase method. Non-oxidized mono-iodinated Aβ monomers were separated by HPLC (as confirmed by MALDI-TOF spectrometry) and used in transport measurements. Transport of intact ¹²⁵I -Aβ40 across the BBB was time- and concentration-dependent in contrast to negligible ¹⁴C -inulin uptake. In 5–6 months old Alzheimer’s Tg2576 mice, Aβ40 BBB transport was increased by >eight-fold compared to age-matched littermate controls, and was mediated via the receptor for advanced glycation endproducts. We conclude the present arterial brain perfusion method provides strictly controlled environment in cerebral microcirculation suitable for examining transport of rapidly and slowly penetrating molecules across the BBB in normal and transgenic mice.