In the present paper, calcium deficient hydroxyapatite (Ca-def OHAP) has been examined in a transmission electron microscope. During the observation, the initial Ca-def OHAP was seen to transform first into a transient intermediate phase, then to a final, stable phase. The intermediate phase is most likely monoclinic and is commensurate with the original Ca-def OHAP phase. Computer images calculated for the hydroxyapatite (OHAP) structure show a structural identity with the initial Ca-def OHAP material. No structural match was obtained for the final and intermediate phases. To our knowledge, this is the first time an intermediate phase is observed during the transformation of Ca-def OHAP. Furthermore, the phenomena observed in this paper are specific to Ca-def OHAP as the damage processes. Under electron irradiation on human tooth enamel crystals or on OHAP ceramics are markedly different from the ones observed here. This is probably indicative of specific structural features of Ca-def OHAP.