A simple, fast and sensitive method for the simultaneous determination of cnidilin and its two metabolites (M1 and M2) in rat bile and stool using HPLC coupled with electrospray ionization tandem mass spectrometry (HPLC-ESI-MS/MS) has been developed. The sample pretreatment was simple, because methanol was the only additive used for dilution of bile and ultrasound of stool. Pimpinellin was used as internal standard (IS). The separation was performed on a reverse phase C18 column with gradient elution consisting of 0.5 parts per thousand aqueous formic acid and methanol (containing 0.5 parts per thousand formic acid). The detection was in the multiple-reaction monitoring mode within 7min. All the analytes were in accordance with the requirement of the validation of the method in vivo (linearity, precision, accuracy, limit of detection and limit of quantification). After oral administrating 24mg/kg of the prototype drug cnidilin, M1 and M2 were determined in bile within 36h, and in stool within 60h. Cnidilin in bile was completely excreted in 24h, and the main excretive amount of cnidilin was 80% in the first 6h, but the drug recovery in bile within 24h was <1.95%. In stool, the main excretive amount of cnidilin was 95.8% in the first 24h, and the drug recovery within 48h was lower than 1.48%. Copyright (c) 2012 John Wiley & Sons, Ltd.