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Ethnopharmacological relevance Geniposide is derived from Gardenia jasminoides Ellis (Rubiaceae). Its anti-inflammatory, antithrombotic effects as well as its preventive effect against ischemic stroke have been reported. Radix notoginseng (Chinese name tienchi or sanqi) is the dried root of Panax notoginseng (Burk.) F.H. Chen, an herb noted for its promotion of blood circulation, blood stasis removal and pain alleviation, and has been widely utilized for the prevention and treatment of microcirculatory disturbances in China and other Asian countries for many years. Notoginsenoside R1 is an effective and structurally representative bioactive constituent of R. notoginseng. In our preliminary study, notoginsenoside R1 was able significantly to improve the bioavailability of geniposide in beagle dogs, but the underlying mechanisms remain unknown. Materials and Methods The present study aimed to investigate the intestinal kinetic absorptive characteristics of geniposide as well as the absorptive behavior influenced by the co-administration of notoginsenoside R1 using an in vitro everted rat gut sac model. Results The results showed good linear correlation between the geniposide absorption in sac contents and the incubation time from 0 to 120 min. The concentration dependence showed a non-linear correlation between the geniposide absorption and the concentrations 0.356–1.424 mg/mL, the absorption was saturated about 1.424 mg/mL. Notoginsenoside R1 at 0.1 and 0.2 mg/mL concentrations was able significantly to enhance the absorption of geniposide (1.424 mg/mL) by 1.7- and 1.4-fold. Moreover, verapamil, a well-known P-glycoprotein inhibitor, was able significantly to elevate the absorption of geniposide 2.4-fold. Notoginsenoside R1 influenced geniposide's absorption in a way similar to that of a P-glycoprotein inhibitor. Conclusions In conclusion, notoginsenoside R1 significantly enhances the intestinal absorption of geniposide. As for the mechanism underlying the improvement of geniposide's bioavailability, it is proposed that notoginsenoside R1 was able to decrease the efflux transport of geniposide by P-glycoproteins.