Even at low fluences doping of quartz by ion implantation results in amorphization. Here we report on the measurement of cathodoluminescence and surface structures during solid phase epitaxy in Na-implanted α-quartz annealed in 18O2 atmosphere. Complete epitaxy was achieved under appropriate conditions of ion fluence, annealing temperature and time. The crystalline structure of the samples was studied by Rutherford backscattering channelling spectroscopy and the 18O-16O exchange between the matrix and 18O2 annealing gas by elastic recoil detection analysis. In the cathodoluminescence spectra taken at room temperature, five bands were identified and assigned to various defect centres. Two of the bands in the violet region at 3.25 and 3.65 eV strongly vary in intensity at 843-1173 K annealing temperature and appear to be intimately correlated with the presence of Na-ions in the implanted region of the matrix. Finally, atomic force microscopy enabled, for the first time, the observation of the correlation of surface structures and epitaxy. © 2006 Elsevier B.V. All rights reserved.