In this study graphite electrodes modified by a thin DNA-imprinted polypyrrole layer, which was able to bind specific target-DNA, are reported. For this aim, electrochemical synthesis of polypyrrole was performed on a pencil graphite electrode by cyclic voltammetry (CV) or by potential pulse sequences (PPS). The modified electrode surface was used for electrochemical determination of target-DNA by differential pulse voltammetry. According to our best knowledge this is a first report on the application of DNA-imprinted polymer for the determination of target-DNA. The results showed that the molecularly imprinted polypyrrole (MIPPy) layer that formed on the carbon electrode surface was sensitive for target-DNA, while the nonimprinted polypyrrole layer was not sensitive to the same target-DNA. Comparison of electrodes modified using PPS and CV techniques is presented. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.