In this study, we performed label-free based CSF quantitative proteomics to identify and analyze the differentially expressed proteins among bacterial meningitis, viral meningitis and hospital controls (children with benign intracranial hypertension). Compared with viral meningitis and hospital controls, we screened 135 differentially expressed proteins to distinguish bacterial meningitis from viral meningitis and controls. Among of them, 69 proteins as potential biomarkers for the diagnosis of bacterial meningitis, including both novel and previously reported candidate protein markers.