Objective To study the pharmacokinetics and cerebrospinal fluid penetration of baicalin in brain edema induced by pertussis bacilli in rabbits. Methods Baicalin concentrations of plasma and cerebrospinal fluid samples were determined by high-performance liquid chromatography. Results In plasma, area under the drug concentration-time curve (AUCp) was 30.63±9.21 μg/ml per hour, half-life (t 1/2p ) was 2.19±0.42 h, and time of maximum plasma concentration (Cmax p) was 56±7.6 μg/ml. In cerebrospinal fluid, AUCcsf was 10.29±5.6 μg/ml per hour, half-life (t 1/2csf ) was 2.31±0.37 h , maximum CSF concentration (Cmax csf) was 2.35±1.23 μg/ml, and time of maximum CSF concentration (tmax csf) was 2.33±0.4 h .The ratio of AUC in plasma and CSF (AUCcsf/AUCp) was 0.32 (>0.2). Conclusions There is a better CSF penetration of baicalin observed in infectious brain edema in rabbits.