Thin films of polyetheretherketone (PEEK) were ion bombarded using a plasma immersion ion implantation (PIII) process in Ar and CH4/O2 plasmas. Free radicals generated by the treatment were detected using electron spin resonance (ESR) spectroscopy. Several types of radicals were observed after the Ar and CH4/O2 PIII treatment, including carbon-centred (alkyl) and oxygen-centred radicals. A higher density of radicals was found after CH4/O2 treatment than after Ar treatment, largely because of an increase in oxygen radicals. The increase in radical intensity was attributed partly to additional radicals contained in a nano-layer deposited by the CH4/O2 PIII treatment. Ar PIII treatment is believed to generate oxygen-containing radicals as a result of reactions with oxygen in the environment. A strong correlation was observed between the free radical density and the autohesive bonding strength developed between two treated PEEK surfaces.