A new HPLC method was developed to separate and identify three polyacetylenes (panaxynol, panaxydol and 1,8-heptadecadiene-4,6-diyne-3,10-diol) found in Panax species. The mobile phase was a linear gradient of 2 : 1 : 3 to 2 : 1 : 1 (v/v/v) methanol/acetonitrile/water in 40 min. HPLC analysis was performed at a flow rate of 1.5 ml/min with UV detection at 254 nm. The contents of the polyacetylenes and ginsenosides in Panax ginseng (white ginseng and red ginseng), P. quinquefolium, P. japonicus, and P. noteginseng were determined using these methods. The species containing the highest polyacetylene content (0.080%) was P. quinquefolium cultivated in Nagano, Japan. Meanwhile, the species with the highest ginsenoside content (9.176%) was P. noteginseng cultivated in Yunnan, China.