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An ultra performance liquid chromatography (UPLC) method was established and validated to simultaneously determine the contents of six aconitum alkaloids in mother, daughter and fibrous roots of 19 batches of Aconitum carmichaelii from Sichuan province. The separation of the six alkaloids was achieved on a ACQUITY UPLC BEH C18 (2.1 mm x 100 mm, 1.7 microm) column at 40 degrees C with a mobile phase consisting of acetonitrile in 30 mmol x L(-1) ammonium acetate buffer solution (adjusted to pH 10.0 with aqueous ammonia) in gradient mode. The data and plots showed that the six aconitum alkaloids have different distributions. Four aconitum alkaloids were almost same in mother and daughter root except benzoylmesaconine and mesaconitine, while the fibrous root differed from the other two roots. The comparisons of significant differences of six aconitum alkaloids between the mother and daughter roots definitely demonstrated that benzoylmesaconine and mesaconitine were the representative components. The 38 detecting samples were classified as two clusters by hierarchical clustering analysis (HCA) and principle component analysis (PCA), the results indicated that the mother root was different from the daughter root on chemical material basis. The study might contribute to the reasonable clinical application of A. carmichaelii.