Results of the studies related to fabrication of sensitive electrochemical biosensor using an interface based on quantum dots (QDs) self-assembly is reported. The QDs assembly is sought to provide improved fundamental characteristics to the electrode interface in terms of electroactive surface area, diffusion coefficient, and electron transfer kinetics. This QDs modified electrode has been utilized to serve as a transducer surface for covalent immobilization of chronic myelogenous leukemia (CML) specific probe oligonucleotide, designed from the BCR-ABL fusion gene. The electrochemical characteristics of this biosensor toward various designed synthetic oligonucleotides reveal a significant enhancement in its mismatch discrimination capability compared to the biosensing assay without QDs under similar experimental conditions. The sensing characteristics of this biosensor offer a potential for detection of target oligonucleotide at a concentration as low as 1.0 pM. Furthermore, the PCR-amplified CML-positive patient samples with various BCR-ABL transcript ratios can be electrochemically distinguished from healthy samples, indicating promising application of the QDs based biosensor for clinical investigations.