The apoptosis of the mice thymocytes was induced with low power helium-neon laser irradiation in vitro. Flow cytomytry analysis of the mice thymocytes was detected by staining cells with a combination of Annexin V-FITC and propium iodide (PI) or rhodamine 123 (Rh123) and PI to show the early event of the apoptosis. The cellular morphology of the staining cells was observed by the transmission electron microscope. The early phase apoptosis of the thymocytes increased obviously after 60 min He-Ne laser (light dose 47.694～51.822 J/cm2) irradiation. With the laser irradiation time prolonged and the light dose increased, the increase of the percentage of the early phase apoptosis of the thymocytes was observed. It shows that the thymocytes after the He-Ne laser irradiation show loss of asymmetry of the phospholipids on the plasma membrane, leading to exposure of phosphatidylserine on the outer surface, that is expressed with the Annexin V positive. The mitochondrial function of the thymocytes is lost, therefore mitochondrial transmembrane potential is markedly decreased. The Rh123 retention is decreased in the mitochondria, and fluorescence intensity is significantly decreased.