Electron paramagnetic resonance studies were conducted on synthetic calcium hydroxy apatite samples co-doped with 239Pu and carbonate ion. These investigations were carried out to assess the self-irradiation effects in bone and teeth on exposure to plutonium, as calcium hydroxy apatite is the major constituent of bone and teeth. On self-irradiation, in addition to the signal from O- ion arising from the radiolysis of hydroxide ion, EPR signals due to CO2-, PO22- and another signal assigned to surface O- ions were observed in the samples. In freshly quenched gamma irradiated samples, signals from CO3-, O- , PO22- and O2- ions were observed. The EPR signal of O2- ion shows a doublet splitting suggesting that O2- ion gets preferentially stabilized close to Pu4+. The radiation damage due to Pu4+ at Ca2+ sites, in the sample appears to be lower as compared to that due to external gamma-irradiation. Moreover, the alpha-dose in 239Pu doped samples has self-annealing effects. These are attributed to localized radiation damage due to alpha-particles compared to evenly distributed radical ions produced due to gamma-irradiation.