Abstract The thermal transformations in phosphorites during flash calcination were investigated by FT-IR spectroscopy, X-ray diffraction and chemical analyses. During flash calcination changes occur, both in the composition of the phosphorite and in the crystallochemistry of the fluor-carbonate-apatite (francolite). The former changes include: decomposition of a great part of the calcite in the rock and oxidation of organic matter. The latter changes include: partial removal of the structural carbonate; partial relocation of the remaining carbonate ions in the apatite structure; a new arrangement of hydroxyl groups and fluorine on the hexagonal axis; partial condensation of the orthophosphate groups and increase of crystallite sizes. Isomorphous substitution of PO4−3 in apatite by SO4−2 and SiO4−4 may take place.