The purpose of this work is to evaluate the long-term effects of radiation on the structure of naturally occurring apatite in the hope of assessing its potential for use as a solid nuclear waste form for actinide sequestration over geologically relevant timescales. When a crystal is exposed to radioactivity from unstable constituent atoms undergoing decay, the crystal’s structure may become damaged. Crystalline materials rendered partially or wholly amorphous in this way are deemed “partially metamict” or “metamict” respectively. Intimate proximity of a non-radioactive mineral to a radioactive one may also cause damage in the former, evident, for example, in pleochroic haloes surrounding zircon inclusions in micas. Radiation damage may be repaired through the process of annealing. Experimental evidence suggests that apatite may anneal during alpha particle bombardment (termed “self-annealing”), which, combined with a low solubility in aqueous fluids and propensity to incorporate actinide elements, makes this mineral a promising phase for nuclear waste storage. Apatite evaluated in this study occurs in a Grenville-aged crustal carbonatite at the Silver Crater Mine in direct contact with U-bearing pyrochlore (var. betafite)—a highly radioactive mineral. Stable isotope analyses of calcite from the carbonatite yield δ18O and δ13C consistent with other similar deposits in the Grenville Province. Although apatite and betafite imaged using cathodoluminescence (CL) show textures indicative of fracture-controlled alteration, Pb isotope analyses of betafite from the Silver Crater Mine reported in previous work are consistent with a model of long term Pb loss from diffusion, suggesting the alteration was not recent. Thus, it is interpreted that these minerals remained juxtaposed with no further metamorphic overprint for ≈1.0 Ga, and therefore provide an ideal opportunity to study the effects of natural, actinide-sourced radiation on the apatite structure over long timescales. Through broad and focused X-ray beam analyses and electron backscatter diffraction (EBSD) mapping, the pyrochlore is shown to be completely metamict—exhibiting no discernible diffraction associated with crystallinity. Meanwhile, apatite evaluated with these methods is confirmed to be highly crystalline with no detectable radiation damage. However, the depth of α-decay damage is not well-understood, with reported depths ranging from tens of microns to just a few nanometers. EBSD, a surface sensitive technique, was therefore used to evaluate the crystallinity of apatite surfaces which had been in direct contact with radioactive pyrochlore, and the entire volume of small apatite crystals whose cores may have received significant radiation doses. The EBSD results demonstrate that apatite remains crystalline, as derived from sharp and correctly-indexed Kikuchi patterns, even on surfaces in direct contact with a highly radioactive source for prolonged periods in natural systems.