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.