The techniques of Fourier transform infrared (FTIR) spectroscopy were applied to analyze the different parts and tissues of Panax Notoginseng (Sanqi, SQ), i.e. rhizome, main root, rootlet, fibrous root, xylem, cambium, phloem and epidermis. Both the FTIR spectra and second derivative spectra of these various parts and tissues of SQ samples were found to be similar. Their dominant component is starch resulting from the characteristic peaks of starch observed at 3 400, 2 930, 1 645, 1 155, 1 080 and 1 020 cm-1 on the spectra of all these SQ samples. However, the varieties of peaks were found on the spectra among these specific samples. The rhizome contains more saponins than others on the basis of the largest ratio of the peak intensity at 1 077 cm-1 to that at 1 152 cm-1. The peaks located at 1 317 and 780 cm-1 on the FTIR spectra of the rhizome and its epidermis indicate that the two parts of SQ samples contain large amount of calcium oxalate, and its content in the latter is relative larger than that in former. The fibrous root contains much amount of nitrate owing to the obvious characteristic peaks at 1 384 and 831 cm-1. For the difference among the various tissues of SQ samples, the peaks at 2 926, 2 854 and 1 740 cm-1 on the FTIR spectra of epidermis is the strongest among the various tissues of main root indicating the largest amount of esters in epidermis. Protein was also found in the cambium of the main root based on the relative strong peaks of amide Ⅰ and Ⅱ band at 1 641 and 1 541 cm-1, respectively. The results indicate that FTIR spectra with its second derivative spectra can show the characteristic of the various parts and tissues of SQ samples in both the holistic chemical constituents and specific chemical components, including organic macromolecule compounds and small inorganic molecule compounds. FTIR spectroscopy is a useful analytical method for the genuine and rapid identification and quality assessment of SQ samples.