The purpose of this retrospective radiographic study was to evaluate and correlate the dimensions and morphology of peri-implant bone defects as determined via cone beam computed tomography (CBCT) scans with regard to the selected treatment approach. Vertical and horizontal peri-implant bone defects (mesial, distal, mesio-oral, mesiobuccal, disto-oral, distobuccal, oral, and buccal) in peri-implantitis cases were measured. Three-dimensional data and defect morphology were correlated to the treatment approach chosen (explantation versus implant retention). A total of 19 patients and 28 implants met the inclusion criteria, resulting in a sample size of 224 sites and a total of 896 measurements. The mean percent bone loss did not correlate to the type of treatment chosen (P = .1286). In contrast, when only the maximum vertical values per implant were selected, maximum percent bone loss exhibited a significant correlation to the type of treatment chosen (P = .0021). The effect of the defect morphology on the treatment strategy chosen did not show a statistically significant correlation (P = .4685). Based on the data presented, the maximum bone loss around the implant seems to be a critical factor in deciding whether or not an implant should be explanted. The use of CBCT for treatment planning in cases of peri-implantitis can offer valuable additional information but should be considered only after initial clinical examination and two-dimensional imaging.