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Surface modification of hydroxyapatite (HA) thin films electrodeposited on titanium was conducted by ion implantation, using nitrogen and argon ions at different constant fluences of 1x10(15), 1x10(16) and 1x10(17) ions/cm(2). SEM and XRD analysis, as well as SRIM calculation, were used to monitor the changes induced by ion bombardment. In the case of HA film implanted with N(4+) ions, the unit cell parameters and unit cell volume increase with increasing nitrogen ion fluences. Similarly, the unit cell parameters and unit cell volume increase after Ar(6+) ions irradiation to a 1x10(15) ions/cm(2). At higher fluences, the unit cell parameters and unit cell volume decrease when argon ion fluences increase to 1x10(16) and 1x10(17) ions/cm(2). These structural changes are consequence of different mechanism of energy transfer of nitrogen and argon ions to HA film. For nitrogen ion irradiation electron energy loss is predominant, while for argon ion irradiation nuclear energy transfer to HA film prevails.