An electrochemical approach for assessing transient DNA transfection efficiency in eukaryotic cells was proposed based on direct analysis of the electrochemical signatures of control and transfected cells in the potential range of (0 ÷ + 1.1) V by the differential pulse voltammetry technique using screen-printed electrodes modified with functionalized carbon nanotubes. The differential pulse voltammetry technique permits to register 4000 cells per electrode. To the best of our knowledge, this will be the first report on the electrochemical registration of transfection process based on comparative analysis of cells. This approach can be used for the incorporation of plasmid pTagGFP2-N with a therapeutically relevant gene without using TagGFP2 as a reporter gene to express green fluorescent protein as a marker in cells. The proposed method was applied to the transfected human breast carcinoma cell line SkBr-3, diploid human fibroblast cell line Wi-38 and normal human CD4+ T lymphocytes. The electrochemical fingerprints of cells demonstrated significant differences in the behavior of transfected cells in comparison with control cells.