Diagenetic effect during burial on the hydroxyapatite in enamel and dentin from fossil human and animal teeth was examined, using X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR). For the enamel and dentin of all fossil teeth, XRD patterns exhibit bulge line and overlap between major reflections of hydroxyapatite, and the crystallinity of hydroxyapatite is low. For each infrared spectrum, H2O and OH(-) have distinct peaks of absorbance, and PO4(3-) and CO3(2-) ions have intensive infrared vibration modes at the fundamental wave numbers. The component of hydroxyapatite of all fossil teeth is similar to the modern biological hydroxyapatite. Furthermore, the index (PCI) which reflects the hydroxyapatite crystallinity of each sample ranges from 2.4 to 4.0 while the index (BPI) reflecting the amount of type B carbonate to phosphate indicates that the values of CO3(2-) content in hydroxyapatite are rather high, accordingly the crystallinity of all fossil hydroxyapatites are poor. It could be concluded that little alteration of hydroxyapatites from fossil human and animal teeth occurred in the process of diagenesis in Jinsha Relict, Chengdu, China.