Polymers with modified surface structure are useful for medicine applications. This study is focused on the surface properties of polymers with carbon layers and their biocompatibility. For experiments was used polyethyleneterephtalate (PET). We used magnetron sputtering for producing of the carbon layers. Raman spectroscopy, goniometry, AFM – microscopy, X-ray diffraction and infrared spectroscopy were used in our experiments to describe the physicochemical properties of modified polymers. Biocompatibility of structure polymer-carbon layers was studied with method in vitro. We investigated adhesion of mouse 3T3-fibroblasts. The carbon layers have positive influence on biocompatibility.