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This paper presents a robust electrochemical detection system composed of microfabricated electrodes and a potentiostat circuit developed for quantitative detection of biomolecules by cyclic voltammetry (CV) measurements. Compared to electrochemical cells employing external counter electrodes (CE) and polymer passivation layers, this system offers more reliable and stable operation owing to on-chip Pt CE and very stable oxide passivation layer, withstanding aggressive cleaning techniques and chemicals involved. The adhesion of oxide to Au and Pt is significantly enhanced by adding slots to the metals and optimizing the metal lift-off process. Different electrode configurations and sizes are tested by CV of redox species before and after self-assembled organic molecular layer formation, and it is concluded that the proposed system offers a low-cost and reliable microelectrode array solution for real time and high sensitive biomolecular detection.