Vinegar and wine processing of medicinal plants are two traditional pharmaceutical techniques which have been used for thousands of years in China. Tetrahydropalmatine (THP), dehydrocorydaline (DHC) and protopine are three major bioactive molecules in Rhizoma Corydalis. In this study, a simple and reliable HPLC method was developed for simultaneous analysis of THP, DHC and protopine in rat tissues after gastric gavage administration of Rhizoma Corydalis. The validated HPLC method was successfully applied to investigate the effect of wine and vinegar processing on the compounds' distribution in rat tissues. Our results showed that processing mainly affect the T(max) and mean residence time (MRT) of the molecules without changing their C(max) and AUC(0-24)( )(h) Vinegar processing significantly increased the T(max) of DHC in heart, kidney, cerebrum, cerebrellum, brain stem and striatum and prolonged the T(max) of protopine in brain. No significant changes were observed on the T(max) of THP in rat tissues after vinegar processing. Wine processing reduced the T(max) of protopine and DHC in liver and spleen and T(max) of protopine in lung, but increased the T(max) of THP in all the rat tissues examined. To our knowledge, this is the first report on the effects of processing on the tissue distribution of the bioactive molecules from Rhizoma Corydalis.