Extracts of the roots of Panax (ginseng) species are analysed using comprehensive two-dimensional gas chromatography. Comparison of comprehensive two-dimensional chromatograms reveals the presence of numerous common components, and possible species-specific components are also observed. Two-dimensional bubble plot presentations of GC×GC(FID) data allow ready qualitative and semi-quantitative comparison of the extracts. The use of GC×GC-quadrupole MS (GC×GC-qMS), operated at a scanning rate of 20 Hz, in conjunction with retention data, permits identification of separated (major) components. Whilst this scan speed will be insufficient for reliable quantitative analysis, considerably improved quality of uncorrected spectra, arising from the enhanced separation over single column GC-MS analysis is apparent. Spectral match qualities of up to 99% are found for a number of components. Comparison of GC×GC-qMS with GC×GC(FID) indicates that good correspondence of peak position patterns is achieved, which aids component identification. It is shown that (quadrupole) mass spectrometric detection is a useful tool for provision of identification of separated compounds in high-resolution comprehensive two-dimensional gas chromatography.