In this work, the presence of structural defects in modified hydroxyapatite (HA) samples were studied. The behavior of HA samples with different chemical compositions was compared. Structural alterations were produced by thermal treatments and high-energy milling. Electron paramagnetic resonance spectroscopy (EPR) was used in order to identify the presence of structural defects. Samples were analyzed at room temperature and the signals observed by electron paramagnetic resonance at g = 1.999 were assigned to oxygen vacancies in the apatitic structure. The determination of vacancy concentration (V-o(.)) in each sample was related with the characteristic parameters of the signal and the experimental conditions. XRD and SEM were used as additional characterization techniques. The production and concentration of these vacancies was correlated to the modifications introduced during the processing of the materials. The results were also related with the chemical composition, particle size and crystallinity of the samples.