Objective To quantify the early apoptosis of gastric cancer cell line SCG7901 induced by 5 FU flow cytometry with Annexin V FITC and PI double labeling. Methods The tumor cells were treated with 5 FU at concentration of 250, 125, 50, and 25 mg/L. The apoptosis was detected 0, 6, 12, 18, 24, 30 h after the treatment by using flow cytometry with Annexin V FITC and PI double labeling method. Results Early apoptosis percentage of tumor cells (0-24 h) was increased significantly with the affected time and the content of 5 FU. But it was decreased during 24-30 h after the treatment, while more necrotic cells were seen at same time. Conclusion 5 FU can induce early apoptosis of tumor cells in a time and dosage depended manner. Annexin V FITC/PI double labeling flow cytometry can distinguish dead cells from early apoptotic cells and be of great use in tumor cell apoptosis quantitative analysis.