Natural apatite samples with different F/Cl content from a variety of geological locations (Durango, Mexico; Mud Tank, Australia; and Snarum, Norway) were irradiated with swift heavy ions to simulate fission tracks. The annealing kinetics of the resulting ion tracks was investigated using synchrotron-based small-angle X-ray scattering (SAXS) combined with ex situ annealing. The activation energies for track recrystallization were extracted and consistent with previous studies using track-etching, tracks in the chlorine-rich Snarum apatite are more resistant to annealing than in the other compositions. ; This research was undertaken on the SAXS/WAXS beamline at the Australian Synchrotron. P.K. acknowledges the Australian Research Council for financial support. A.N. would like to acknowledge the Universiti Teknologi MARA (Malaysia) and Ministry of Higher Education, Malaysia for financial support.