Objective To explore the significance of changes of matrix metalloproteinase-9(MMP-9), interleukin-6(IL-6), and tumor necrosis factor-alpha(TNF-α) protein level in the cerebrospinal fluid (CSF) of children with viral encephalitis(VE). Methods The concentration of neuron-specific enolase(NSE), structural proteins 100B (S100B), and MMP-9, IL-6, TNF-α in the CSF of VE children were detected by an enzyme linked immunosorbent assay, and the correlations of them were analyzed. Results NSE, S100B, MMP-9, IL-6, TNF-α protein expression could be found significantly higher than those in the control group, and there were significant differences according to statistics expression trends(all P<0.05). The NSE protein expression was significantly positive related with S100B in the VE group (r=0.467, P=0.009), and the concentration was markedly negative related with the duration of viral encephalitis (r=-0.472, P=0.008). MMP-9, IL-6 protein expression were significantly positive related with NSE, S100B respectively (r=0.698, P=0.00; r=0.559, P=0.00; r=0.812, P=0.00; r=0.664, P=0.00). TNF-α protein expression was positive related with CSF S100B(r=0.363, P=0.049), but there was no correlation between TNF-α and NSE(r=0.245, P=0.193). Conclusions The neurons and the neuroglial cells are damaged in the viral encephalitis children.MMP-9, IL-6, TNF-α protein may participate in the pathological damage process of nerve cells in VE children in different degrees. Key words: Viral encephalitis; Structural proteins 100B; Matrix metalloproteinase-9; Interleukin-6; Tumor necrosis factor-alpha; Child