Using X-ray fluorescent computed tomography (XFCT), the in vivo and ex vivo cerebral distribution of a stable-iodine-labeled cerebral perfusion agent, iodoamphetamine analog ((127)I-IMP), has been recorded in the brains of mice. In vivo cerebral perfusion in the cortex, hippocampus and thalamus was depicted at 0.5 mm in-plane spatial resolution. Ex vivo XFCT images at 0.25 mm in-plane spatial resolution allowed the visualisation of the detailed structures of these regions. The quality of the XFCT image of the hippocampus was comparable with the (125)I-IMP autoradiogram. These results highlight the sensitivity of XFCT and its considerable potential to evaluate cerebral perfusion in small animals without using radioactive agents.