The analysis method of gentiopicroside(GPS) in mice blood and tissues was established, the pharmacokinetics and tissue distribution of GPS in mice after orally and intravenously administration were investigated. The solid phase extraction(SPE) column was selected for pre-dealing with serum and tissue exponent, and the RP-HPLC was employed to determine GPS concentration in blood and tissue following with theophylline as internal standard. A linearity was obtained from 1 to 68 mug/mL of GPS in serum and tissue with a good correlation coefficient (r = 0.9996). The mean recovery ratioes for serum and tissue were 97.15% +/- 1.33% and 94% similar to 110%, respectively. The relative standard deviations (RSD) for intra-precision and extra-precision were lower than 6%, respectively. The results show: the disposal process of GPS in mice after oral and injection of vein administration are fitted to two compartments open model; the half lives of GPS are 6.099 and 2.813 h for intravenously and orally administration, respectively; the T-max of GPS after orally administration is 0.495 h, and the bioavailability is 39.62%; the AUC gradient in individual tissue following orally administration is kidney, serum, liver, spleen, lung, thymus, fat, heart, muscle, stomach, intestinal, brain; the MRT gradient is muscle, serum, lung, spleen, intestinal, heart, stomach, brain, liver, thymus, kidney, fat. GPS can be absorbed quickly in mice, but with a lower bioavailability. GPS can distribute to tissue extensively, but with short MRT. The slow release formulation ought to be an ideal dosage formulation for GPS.