OBJECTIVE To investigate the in situ absorption kinetics of berberine (BER) and jatrorrhizine( JAT) at different intestine segments in rats. METHODS The intestinal perfusion experiment was performed on rats in vivo to observe the effects of absorption sites and drug concentration on the intestinal absorption characteristics of BER and JAT. RESULTS The apparent absorption rate constants (Ka) of BER and JAT at duodenum, jejunum, ileum and colon were 0.1540, 0.1160, 0.9793, 0.6795 h(-1) and 0.0743, 0.0564, 0.0456, 0.0234 h(-1), respectively. The absorption of BER and JAT decreased according to the turn of duodenum, jejunum, ileum and colon. Compared to the lower segment, BER and JAT were better absorbed at the upper and middle segments of intestine in rats. The Ka of BER and JAT had no significant difference when the concentration of the extractive Rhizoma Coptidis was at 22-88 mg x L(-1). However, the absorption quantity of BER and JAT were proportional to the concentration respectively and the saturated phenomena were not observed. CONCLUSIONS Both the BER and the JAT is can be absorbed in whole intestine and the results indicated that the absorption of BER and JAT compiled with the first order kinetics through passive diffusion mechanism.