To investigate the relationship between protein aggregation and delayed neuronal death, we adopted rat models of 20 min ischemia. Brain ischemia was produced using the 2-vessel occlusion (2VO) model in rats Light microscopy, transmission electronic microscopy and Western blot analysis were performed for morphological analysis of neurons, and protein detection. The results showed delayed neuronal death took place at 72 h after ischemia-reperfusion, protein aggregates formed at 4 h after reperfusion and reached the peak at 24 h after reperfusion, and Western blot analysis was consistent with transmission electronic microscopy. We conclude that protein aggregation is one of the important factors leading to delayed neuronal death.