To evaluate the method of measuring apoptosis by flow cytometry with three stains, the apoptosis percentage of rat cortical neurons was measured by flow cytometry using propidium iodide(PI) staining, Annexin V/PI and JC-1 double staining respectively. The results showed that: the apoptotic positive percentage measured by PI staining,Annexin V/PI and JC-1 was 2.60%,6.52% and 18.56%, respectively. Our conclusion is that there were significant differences among the results of three staining methods: JC-1 staining was the most sensitive method, whereas PI single staining was not suitable to measure the early apoptosis of cells.