A monomeric complex of Cu(II) with Ornidazole was synthesized and characterized. Electrochemical reduction of the complex, by maintaining a glassy carbon electrode in aqueous solution, at its cathodic potential, under de-aerated (Argon saturated) condition, generates different products. Such electrochemical reduction was carried out at different times in presence of either nucleic acid bases or calf thymus DNA. Since the nitro-radical anion (NO2−) and other reduction products of 5-nitroimidazoles or their complexes are crucial for biological activity, attempt was made to follow the interaction of electrochemically generated reduction products of the complex with nucleic acid bases or with DNA to realize what happens when these drugs enter the cells of a target organism, get reduced enzymatically and show activity that lead to cell death. The study reveals that the monomeric complex of Cu(II) with Ornidazole was better in causing modification of nucleic acid bases and to double strands of calf thymus DNA when compared with Ornidazole under identical experimental conditions. While Ornidazole was more effective on guanine and cytosine than thymine or adenine, the complex was found more effective on cytosine than thymine and adenine. For the complex, experiments with guanine could not be done because of a physical association between the two that turned the solution turbid, preventing the experimental protocol from being correctly implemented. In general, damage caused to nucleic acid bases or to calf thymus DNA was greater for the complex than for Ornidazole. This was correlated with results obtained for calf thymus DNA, providing a preliminary idea regarding the type of DNA (based on nucleic acid base composition) that is most likely to be affected by these compounds. The study also correlates the fact why organisms with a reasonably high GC content in their DNA have been reported to succumb to such compounds. It clearly indicates Ornidazole and its Cu(II) complex have a somewhat higher tendency to affect GC sites than AT. In brief, the study of in situ reactivity of electrochemically generated reduction products on Ornidazole and its Cu(II) complex with nucleic acid bases and calf thymus DNA reveal why literature shows Ornidazole to be active on GC rich DNA containing organisms.