When cultivated with Aspergillus niger, geniposide, an important drug, is transformed into genipin and genipinine. A simple and rapid HPLC method for simultaneous determination of geniposide and its two metabolites in broth of A. niger is described. The chromatographic separation was achieved on a C18 ODS column (250 x 4.6 mm) by gradient elution with 0.1% formic acid in water and 0.1% formic acid in acetonitrile as the gradient mixtures. The flow rate was 1 mL/min, the detection wavelength was 238 nm and the column temperature was kept at 28 degrees C. The retention times of geniposide, genipin and genipinine were 10.9, 13.8 and 21.5 min, respectively. The mean absolute recoveries of three analysts were over 98%. Quantification limits were 0.01 microg/mL for geniposide and 0.02 microg/mL for the two metabolites. The method was applied for the quantification of geniposide, genipin and genipinine during fermentation and the evaluation of the bioavailabilities of these three compounds in Caco-2 monolayer.