Objective To evaluate the relationship between changes of cerebrospinal fluid (CSF) or blood S - 100 protein (S- 100), neuron specific enolase (NSE) levels and the severity of hypoxic - ischernic encephalopathy (HIE), and to explore the mechanism of changes of these protein levels. Method Seven - day postnatal SD rats were used. Their serial blood and CSF S - 100 and NSE were measured by radioimmunoassay. By using the RT - PCR technique the expression of mRNA for S - 100 and NSE in the brain tissue at different gluts of time after HI injury was tested. Immunohistochemical assay was used to investigate the changes of the expression of S - 100 and NSE at the protein level. Results The values of S - 100, NSE were (1. 205 ± 0. 183) μg/L and (3. 97 ± 0. 228) ηg/ml respectively at 24 hours and (1. 235 ± 0. 097) μg/L, (3. 76 ± 0. 234) ηg/ml respectively at 48 hours in the blood, were(1. 28 ± 0. 031 ) μg/L, (7. 15 ± 0. 717) ηg/ml respectively at 24 hours and (1. 32 ± 0. 097) μg/L, (4. 29 ± 0. 144)ηg/ml respectivaly at 48 hours in the CSF after HI injury. The values of S - 100, NSE were increased significantly in both the blood and CSF samples during 24-48 hrs after HI inujry than in the control group (0. 645 ± 0. 05 μg/L, 3. 15 ± 0. 164 ηg/ml and 0. 68 ± 0. 059 μg/L, 3. 42 ± 0. 322 ηg/ml respectively). The increment corresponded well with death cell counts in the brain after HI injury; a peak of rnRNA expression of NSE exnerged at 24 hours after HI injury, while S- 100 mRNA occurred at 48 hours. The positive area of the expression of S - 100 at the protein level increased progressively during 12-96 hrs, but the expression of NSE decreased significantly with the lapse of time. Conclusions S - 100 and NSE are senstitive markers for hypoxic-ischemic brain damage(HIBD). The appropriate time for sample collection is 24 - 48 hrs after HI injury. The mechanism of S - 100 level increase in the blood and CSF after HI injury is not only due to the leakage from damaged brain cells but also through a high expression Of S - 100 mRNA and S - 100 protein, while the elevation of NSE in the blood and CSF was mainly due to the leakage from neuronal damage.