The mechanism of the carbonate substitution in the apatite structure is unraveled through analysis of Rietveld refinements of powder diffraction data from a single-phase natural carbonate fluorapatite (francolite). The refined values of the P-O bond lengths give a ~1.6% distortion of the phosphate tetrahedron caused by the carbonate substitution. The two bond lengths P-O1 and P-O2 and their corresponding angles on the mirror plane of the phosphate tetrahedron are mainly disturbed by this substitution. A static positional disorder, mainly of the atoms at the tetrahedral sites, is revealed from the temperature dependence of the atomic anisotropic displacement parameters. A model for the mechanism of the carbonate entrance in the apatite structure is proposed.