Gentiana Radix is one of the most often used drugs in traditional Chinese medicine. Stir frying with yellow wine is the most common processing method. To clarify the principle of processing, an experiment was carried out to compare the tissue distribution of the typical constituent after oral administration of raw G. Radix and wine-processed one. To compare the tissues distribution of gentiopicroside oral administration of raw and wine-processed G. Radix, High-performance liquid chromatogram with ultraviolet detection was developed and validated for the determination of gentiopicroside in heart, liver, spleen, lung, kidney, stomach, small intestine and large intestine tissues. The gentiopicroside in raw and wine-processed G. Radix was distributed in all tissues involved in this study. Compared with the rats administration of raw G. Radix, the proportions of gentiopicroside in heart, liver and lung tissues increased in rats with administration of wine-processed one. The proportion of gentiopicroside in upper-JIAO and liver tissue can be increased by wine-processing.