Rutile (TiO2) single crystals with (110) and (100) orientations were irradiated with 360 keV Xe2+ ions at 300 K to fluences ranging from 1×1017 to 5×1020 Xe/m2. Irradiated samples were analyzed using Rutherford backscattering spectroscopy combined with ion channeling analysis (RBS/C) and transmission electron microscopy (TEM). RBS/C results showed that much of the instantaneous displacement damage produced under ion irradiation is recovered under ambient temperature irradiation conditions. Upon irradiation to a fluence of 2×1019 Xe/m2, the radiation damage-induced microstructure was observed by TEM to consist of three distinct layers: (1) a layer near surface (thickness about 12 nm) exhibiting relatively homogeneous TEM contrast; (2) a second layer with a low density of relatively large-sized defects; and (3) a third layer consisting of a high concentration of small defects. After the fluence was increased to 5×1019 Xe/m2, a buried amorphous layer was observed by TEM. The thickness of the amorphous layer was found to increase with increasing Xe ion fluence. The uppermost damage layer, which accounts for the surface subpeak in RBS/C spectra, was found to be polygonized by ion irradiation.