Background: Quiet a number of researches has reported the morphological changes of global ischemic reperfusion model. However, there are few reports on the ultrastructural changes of cortex in early reperfusion, especially the change of blood brain barrier. Objective: To explore the changes of brain cortex neurons, glial cells and blood brain barrier in order to provide reliable evidence for clinical treatment. Design: A randomized and controlled trial. Setting: Department of Neurosurgery, Department of Anesthesia and Electron Microscope Room of Beijing Tiantan Hospital. Materials: The experiment was conducted to 6 Wistar rats in Beijing Neurological Surgery Research Institute of Capital University of Medical Sciences during February 2003 to February 2004. The rats were randomly divided into two groups with one of ischemia-reperfusion group and sham operation group with 3 rats in each group. Interventions: To prepare global ischemic reperfusion model of rats. Brain was removed from ischemic group in one hour of reperfusion and from sham operation group one hour after the operation. Electronic microscope technique was used to observe the ultrastructural changes of cortex. Main outcome measures: Ultrastructural changes of cortex. Results: The neurons of cortex shrank to certain degree in the early stage of ischemic reperfusion (1 hour). The glial cells were swollen with dissolved chromosome in nucleus and unclear nuclear membrane. The foot protrusions around blood vessel slightly swelled and separated from basement membrane. Mircro-tubes were partially dissolved. Conclusion: In early stage of reperfusion injury, the cortex neurons, glial cells, cellular framework and blood brain barrier already changed which suggested that the protective treatment such as reducing brain edema, protecting blood brain barrier should start as early as possible.