Ion implantation at 25 and 100 keV has been used as a tool for the modification of the surface properties of two biomedical polymers. The modulation induced by the different energy dispersion mechanisms of Ar and He have allowed satisfactory modifications for both the activation of the surfaces of chemically functional polycaprolactone (PCL) and the stabilization of anti-fouling poly(ethylene glycol) (PEG). In both cases the implantations have been performed at doses of 10 14 cm Γ2 by taking into account the effect of different current densities, which are shown to distinctly influence the fragmentation-crosslinking of the target polymers. The resultant films were characterized by Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, time of flight secondary ion mass spectroscopy and atomic force microscopy. Both shifts in zeta potential versus pH curves and the alteration of the polar components of the surface free energy (contact angle measurements) were correlated with the composition analysis. The response of the modified surfaces towards biomolecular interaction is demonstrated by the induction of preferential adsorption on irradiated PCL and the inhibited adsorption onto implanted PEG regions for selected oligopeptides and proteins.