Oligodeoxynucleotides (ODNs) containing adenines (A), cytosines (C) and guanines (G) are electroactive species and produce cathodic (A,C) and anodic (G) voltammetric peaks at mercury electrodes. The reduction peak potentials of A and C are located very close to each other, so that usually only one voltammetric peak is observed. One signal only can be observed even when adsorptive transfer stripping voltammetry (AdTSV) is used. The elimination voltammetry with linear scan (EVLS) used in connection with a hanging mercury electrode is able to distinguish between A and C signals. The EVLS is based on elimination of one or two selected currents from total currents measured by linear scan voltammetry. The function eliminating kinetic and charging currents, and conserving the diffusion current was calculated for the case of adsorbed electroactive substance, and the theoretical elimination curve has a peak-counterpeak form. Various elimination functions were applied in the analysis of oligonucleotides containing different contents of A, C and G, their sequences, and length of ODNs. The height and potential of EVLS signals were affected by pH, buffer components, content of bases, and time of accumulation. Our results showed that the voltammetric signal of the bases can be separated, and that EVLS in connection with AdTSV is a promising tool for qualitative and quantitative studies of not only homo-ODNs but also hetero-ODNs, including hairpins.