MgO(100) single crystals are implanted with 1.50-MeV Al+ and 3.00-MeV A2+ ions at a fluence of 1 × 1015 Al atoms cm-2 under high-vacuum conditions. The surface morphology of the substrate is measured in air using atomic force microscopy and X-ray reflectometry followed by computer-simulated spectrum analysis. The ion-irradiated areas are found to protrude to different heights on the nanometre scale. Small height differences are observed in the areas irradiated by Al+ and Al2+ ions of comparable energy, dose rate and total fluence. The results indicate that protrusions are most likely caused by implantation-induced point defects (vacancies) generated in the crystal during implantation. Other possibilities for the cause of protrusions are discussed. Thermal treatment stimulates a partial recovery of the implantation damage and alters the topography of MgO surfaces.