A thermally stimulated depolarization currents (TSDC) study in natural fluorapatite single crystals has established different relaxation mechanisms for two polarization orientations (Ep parallel and perpendicular to the crystallographic c axis), which are discussed in relation to the defect chemistry and the specific columnar structure in apatite. The intensities of the thermostimulated current signals between the two poling field orientations demonstrate a difference of at least one order of magnitude, with the higher one recorded for the electric field parallel to the c axis. The TSDC thermogram appearing with the electric field parallel to c axis, in the 10–320 K range, consists of a broad and complex band (HT), with a maximum around 300 K. The relative intensity of associated current signals is indicative of extensive dipole-like ionic motions along c axis with a distribution in their activation energies ranging between 0.14 and 0.85 eV. The microdomain structure of fluorapatite along c axis permits the formation of charge layers at the interfaces. After annealing, the induced changes of size and/or shape of the interfaces could explain the observed changes of band intensity and location. With the electric field perpendicular to c axis, the spectrum consists of at least five well-defined relaxation bands, the high temperature ones (HT1, HT2, HT3) decreasing after heating at 673–873 K. The most dramatic change was recorded for an intermediate LT2 single-relaxation band located around 185 K, with a high activation energy of 1.06 eV, which manifested a significant growth after annealing. Rietvelt analysis of the x-ray diffraction patterns of the original and annealed apatite powders, indicates- change in the unit cell parameters of the hexagonal structure (i.e., a increases from 9.3921 to 9.3940 Å after annealing), which can be related to the establishment of a new equilibrium distribution of the abundant trivalent rare-earth (Ce, La, Nd, Pr,…) impurity ions. The origin of the TSDC bands is discussed and tentative correlations are suggested, in terms of substitute aliovalent ions-vacancy dipoles. The thermal response of the high temperature relaxation bands in the case of Ep⊥c axis, is characteristic of dipole clustering phenomena—although an explanation based on localized changes in the structural environment of the pertinent dipoles/ions cannot be disregarded. © 1999 American Institute of Physics.