The contamination of water and soil with heavy metals such as lead and cerium, is a major global problem. Hydroxyapatite with the stoichiometric formula Ca10(PO4)6(OH)2 could be a potential candidate for lead or cerium immobilization. This study focuses on the structural characterization of cerium and lead doped hydroxyapatite synthesized using two different methods: incipient wetness impregnation (IWI) and ion exchange (IE) under varying concentrations of Ce and Pb. X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR) and Scanning electron microscope (SEM) were used to understand the incorporation and/or the deposition of lead or cerium on the surface of calcined or uncalcined hydroxyapatite. Results show that cerium is deposited on the surface of the hydroxyapatite in the form of cerium hydroxy nitrate (Ce(OH)(NO3)2) for samples synthesized by IWI. However, the calcination of these samples led to the formation of CeO2. In the case of samples synthesized by ion exchange cerium is efficiently hosted in hydroxyapatite under a solid solution at a low level (<3%) but forms isolated Ce-oxide at a high level. The XRD spectra show that for powders doped with more than 0.6% Pb, characteristic peaks of PbO and Pb(NO3)2 appear respectively with the calcined and uncalcined powders prepared by the IWI method. XRD characterization showed the formation of PbHPO4 and Pb-HAP for samples synthesized by ion exchange (IE). This work indicates the excellent insertion potential of cerium or lead ions in hydroxyapatite-based matrices suitable for various applications such as energy, biomedical, catalysis, and environmental sciences.