A sensitive method for quantitating the pharmacologically active polyacetylenes panaxynol and panaxydol in Radix Ginseng was developed using a capillary gas chromatography-mass spectrometric (GC-MS) method. The detection mode of selected ion monitoring (SIM) allowed sensitive and selective quantitation of the two compounds in ginseng. Method validation showed that the GC-MS method has much lower detection and quantitation limits than the high-performance liquid chromatography (HPLC)-UV method. This indicates that GC-MS is particularly useful for the analysis of polyacetylene compounds, which have relatively low abundances compared with ginsenosides in ginseng. Based on the quantitative results of different types of ginseng herbs, it was found that the panaxydol and panaxynol contents were higher in forest ginseng than in cultivated ginseng. This method was further applied to the quantitative analyses of panaxynol and panaxydol in Radix Notoginseng and American ginseng. The ratio of panaxydol to panaxynol can be utilized as a marker for differentiating ginseng, notoginseng, and American ginseng. This study introduces the first GC-MS method for the quantitative analysis of polyacetylenes in herbs of the Panax genus.