Hydroxyapatite (HAp) phantoms have been proposed as an alternative to plaster of Paris (poP) phantoms for the calibration of x-ray fluorescence-based systems for the in vivo quantification of bone lead and strontium which employ a coherent normalization procedure. The chemical composition of the material becomes critical in the calculation, or omission, of the coherent correction factor (CCF) required in this normalization procedure. This study evaluated the long-term chemical stability of HAp phantoms. Phantoms were prepared and allowed to age for a two week period and over a seven year period in ambient conditions. The chemical composition of the phantoms was then assessed by powder x-ray diffraction. Two week old phantoms were found to be composed of HAp with only a small amount of contamination from CaHPO4·2H2O. Seven year old phantoms were found to have converted nearly completely to a carbonate-bearing apatite in the form of Ca10(PO4)6(CO3)0.75(OH)0.5 indicating that the HAp phantom material likely reacts with carbon dioxide in air over time forming a carbonate-bearing apatite. The influence of this chemical conversion was assessed at the level of relevant cross-sections. Calibration under the assumption that the material is HAp when in fact it is a carbonate-bearing apatite would result in not more than a 0.2%–2% bias in the total mass attenuation coefficient within the photon energy range of 0–100 keV. Differential scattering cross-section for coherent scattering was found to differ between HAp and carbonate-bearing apatite by 0.9%–2% for both a 35.5 keV and 88.0 keV γ-ray. This variation in the differential scattering cross-section for coherent scattering may introduce a ca. 2% bias in the CCF used within the coherent normalization-based calibration procedure. Using HAp phantoms as calibrators thus requires acknowledgement of this conversion in chemical form and possible introduction of uncertainty into the calibration procedure.