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The purpose of this study is to develop biocompatible and conducting coating being carrier of biologically active compounds with the potential use in neuroprosthetics. Conducting polypyrrole matrix has been used to immobilize and release model drugs, quercetin and ciprofloxacin. Two routes of immobilization are described: drugs have been incorporated in the polymer matrix in the course of the electropolymerization process or after polymerization, in the course of polymer oxidation. Using UV/Vis spectroscopic detection we demonstrate that both immobilization approaches display different drug-loading efficiencies. In the case of ciprofloxacin, drug incorporation following synthesis is a more efficient immobilization approach (final drug concentration: 43.3 (± 9.5) μM/cm²), while for quercetin the highest loading is accomplished by drug incorporation during synthesis (final drug concentration: 29.1 (± 5.9) μM/cm² …