The chemical characteristics for different parts of Panax notoginseng, including root, fibre root, rhizome, stem, leaf, flower and seed, were determined using high performance liquid chromatography-evaporative light scattering detection (HPLC-ELSD) and pressurized liquid extraction (PLE). Eight major saponins, namely notoginsenoside R1, ginsenosides Rg1, Re, Rb1, Rc, Rb2, Rb3 and Rd were also quantitatively compared among the different parts of P. notoginseng. The chromatograms showed that there was significant difference between underground (root, fibre root, rhizome) and aerial (leaf and flower) parts from P. notoginseng, though the similarities of entire chromatographic patterns among tested samples from underground (0.965 ± 0.029, n = 12) and aerial parts (0.987 ± 0.014, n = 5) were similar, respectively. Especially, no saponin was detected in the seed of P. notoginseng. Hierarchical clustering analysis based on eight investigated saponins or the ratios of contents for ginsenoside Rg1/Rb1 and ginsenoside Rb3/Rb1 showed that the samples from different parts of P. notoginseng were divided into three main clusters. One cluster was underground parts, which contained rich protopanaxatriol and protopanaxadiol types saponins. The leaf and flower were in the same cluster, which contained protopanaxadiol type saponins only. Especially, ginsenoside Rc, Rb2 and Rb3, rare in the underground parts, were rich in aerial parts of P. notoginseng. The stem of P. notoginseng was another cluster. Based on the cluster analysis, the chemical characteristics for different parts of P. notoginseng were revealed. They are composite cluster (underground parts), protopanaxadiol cluster (aerial parts) and interim (stem) cluster, which was the one between the two typical clusters, respectively. The result shows that chemical characteristics of underground parts and aerial parts from P. notoginseng are obviously different, which is helpful for pharmacological evaluation and quality control of P. notoginseng. © 2006 Elsevier B.V. All rights reserved.