All artificial materials used for implantation into an organism cause a foreign body reaction. This is an obstacle for a number of medical technologies. In this work, we investigated the effect of high-energy ion bombardment on polyurethane for medical purposes and the reaction of body tissues to its insertion into the mouse organism. An analysis of the cellular response and shell thickness near the implant showed a decrease in the foreign body reaction for implants treated with high-energy ions compared to untreated implants. The decrease in the reaction is associated with the activation of the polyurethane surface due to the formation on the surface layer of condensed aromatic clusters with unbonded valences on the carbon atoms at the edges of such clusters and the covalent attachment of the organism's own proteins to the activated surface of the implant. Thus, immune cells do not identify the implant surface coated with its own proteins as a foreign body. The deactivation of free valences at the edges of aromatic structures due to the storage of the treated implant before surgery reduces surface activity and partially restores the foreign body response. For the greatest effect in eliminating a foreign body reaction, it is recommended to perform the operation immediately after treating the implant with high-energy ions, with minimal contact of the treated surface with any materials.