The work is to study the expression of NSE and S-100 protein in SD rat brain tissue irradiated by 6MeV electron beam. The whole brain of the Sprague-Dawley rats were irradiated with single dose of 10Gy, 20Gy and 30Gy by 6MeV electron. Immunohistochemical method was used to measure the contents of S-100 and NSE in brain tissue. One-ANOVA was used for analysis. The expression of S-100 and NSE after whole brain irradiation was time-dependent. Compared with that of control group, there was an increase of expression of S-100 D7 after irradiation during the observed time (,p,<,0.05). On the contrary, there was a decrease of NSE 24h after radiation, disappearing nearly at D30 (,p,<,0.05). The indexes above were changed with the different dose levels at 7d after radiation. Radiation can induce the expression of S-100, as well as inhibit the expression of NSE on radiation-induced acute brain injury. The changes of the expression of S-100 and NSE on the brain can act as indexes of acute brain injury induced by radiation.