The stability of thermally processed hydroxyapatite coatings for oral and orthopedic bioprostheses has been questioned. Information on the chemical changes, which occur with hydroxyapatite biomaterials post-implantation in humans, is lacking. The purpose of this investigation was to begin to examine post-implantation surface changes of hydroxyapatite-coated implants using scanning electron microscopy (SEM), x-ray microanalysis (EDAX), Fourier transform infrared spectroscopy (FTIR), and x-ray diffraction (XRD). Three retrieved dental implant specimens from humans following clinical failure due to peri-implantitis were examined. Unimplanted cylinders served as controls. Clinically, the retrieved specimens were all enveloped by a fibrous tissue capsule with bone present at the apical extent of the implant. SEM analysis showed that the retrieved surfaces were coated with both calcified and proteinaceous deposits. EDAX scans of the retrieved specimens demonstrated evidence of hydroxyapatite coating loss reflected by increasing titanium and aluminum signals. Other foreign ions such as sodium, chloride, sulfur, silica, and magnesium were detected. XRD of the control specimens showed that the samples were predominantly apatite; however, two peaks were detected in the diffraction pattern, which are not characteristic of hydroxyapatite, indicating that small amounts of one or more other crystalline phases were also present. The retrieved specimens showed slightly larger average crystal size relative to the control sample material, and the non-apatite lines were not present. FTIR evaluation of the retrieved specimens revealed the incorporation of carbonate and organic matrix on or into the hydroxyapatite. Narrowing of and increased detail in the phosphate peaks indicated an increase in average crystal size and/or perfection relative to the controls, as did the XRD results. Based on these results, we conclude that chemical changes may occur within the coating, with the incorporation of carbonate and concomitant reduction in hydroxyapatite coating thickness. Thermodynamic dissolution-reprecipitation of the coating itself and subsequent surface insult by bacterial and local inflammatory components may be involved with these changes.