Background: Desflurane can decrease the hyponeuria of incomplete cerebral ischemia-reperfusion of rat models. But there is not enough evidence to show morphologically its brain protective effect. Objective: To observe the influence of desflurane on the ultrastructure of global cerebral ischemia-reperfusion in rats and study its effect on brain protection. Design: Randomized and controlled study. Setting: Beijing Tiantan Hospital of Capital University of Medical Sciences. Materials: The experiment was carried out in the Beijing Institute of Neurosurgery of Capital Medical University. The nine Wistar rats were randomized into 3 groups: ischemia group(n = 3), desflurane group(n = 3), and sham-operation group(n = 3). Interventions: Rat models with global cerebral ischemia-reperfusion were prapared. The desflurane inhalation for one hour was given immediately to the desflurane group when the reperfusion started. The brain was obtained one hour after the ischemia-reperfusion in the ischemia and desflurane groups and after the operation in the sham-operation group. The changes of cortical ultrastructure were observed with electron microscope. Main outcome measures: The changes of cortical ultrastructure. Results: The pyknosis of neurons in the desflurane group was less, and the organelle and microtubulo-structure were basically normal, but the gliocytes and microcirculation were not improved, as compared with those of the ischemia group. Conclusion: Desflurane may have protective effects on neurons and cytoskeletons, but not on the gliocytes and microcirculations.