Abstract: Twenty-four apatite (Ap) samples mainly from carbonatite and alkaline rocks were studied by electron microprobe, IR spectroscopy and X-ray powder diffraction. The crystal structures of six were refined using single crystal X-ray diffraction data to R = 1.7–2.5%. The generally high Si content of Ap from carbonatite and alkaline rock has been related to the presence of characteristic Si-O absorptions in IR spectra. Bands, whose intensities change with Si content, were observed at 520, 650, 930 and 1160 cm−1. The IR absorption features of ν3 CO3 mode of Ap from carbonatite are different from those of v3 CO3 mode of Ap from sedimentary rock. This phenomenon is probably due to the different effects of F and OH on the CO3 substitution for PO4. The structural refinements yield more information on the CO3=PO4 substitution, which is now supported also by the geometrical evolution of the tetrahedron with increasing CO3 content: the tetrahedral size decreases and the angle distortion increases with C-content. It is likely that the triangular planar CO3 group is disordered on the four faces of PO43− tetrahedron. It was observed also that Ap from early-stage carbonatite is OH-dominant with considerable LREE, Si, CO3 and negligible Mn, Fe, Mg, K, S and C1 contents. They have high Sr/Mn, Si/S and C/S ratios.