Polyaniline (PAni) nanofibers doped with HCl and CSA have been irradiated with 90 MeV O(7+) ions with fluence of 3 x 10(10), 3 x 10(11) and 1 x 10(12) ions cm(-2). TEM micrographs show a decrease in the fiber diameter with increasing irradiation fluence, which has been explained on the basis of the Coulomb explosion model. XRD analysis reveals a decrease in the crystalline domain length and an increase in the strain. The increase in d-spacing for the (100) reflection with increasing irradiation fluence is ascribed to the increase in the tilt angle of the polymer chain, which is also evident from micro-Raman spectra. UV-vis spectra of the PAni nanofibers exhibit blue-shift in the absorption bands attributed to pi-pi* band transitions indicating a reduction in particle size after SHI irradiation; as also observed in TEM micrographs. Micro-Raman spectra also reveal a transition from the benzenoid to quinoid structures in the PAni chain as the fluence is increased. Although the quinoid unit has no hydrogen for DPPH scavenging, the antioxidant activity of PAni nanofibers is found to increase with increasing fluence. This has been attributed to the availability of more reaction sites as a result of fragmentation of the PAni nanofibers which compensates for the benzenoid to quinoid transition after irradiation. The biocompatibility of the PAni nanofibers is also found to increase with increasing irradiation fluence, indicating the possibility of employing swift heavy ion irradiation as an effective technique in order to modify conducting polymer nanostructures for biomedical applications.