The Scanning electrochemical microscopy (SECM) is used to selectively detect intervening mismatches and abasic sites within monolayers of ds-DNA self-assembled onto gold electrodes. The electrocatalytic cycle involving oxidation of leucomethylene blue (LB), an electrochemically reduced form of methylene blue intercalated within the ds-DNA monolayer self-assembled on gold electrode, by the SECM tip-generated Fe (CN) 6 3-allows regeneration of LB via long-range heterogenous electron transfer mediated by the DNA π-stack. Monolayers featuring disruptions in the DNA π-stack via a single-base mismatch or abasic site exhibit strongly attenuated methylene blue electrochemistry within the DNA film leading to a disruption of the catalytic cycle, thereby diminishing the SECM tip current. The inherent differences in catalytic tip currents can be used to distinguish monolayer domains containing native ds-DNA versus ds-DNA containing π-stack lesions within the micron-level lateral spatial resolution of SECM. The analogous catalytic cycle between Ru (NH3) 6 2+ attached to the ds-DNA via electrostatic interactions with backbone phosphates and SECM tip generated Fe (CN) 6 3-is insensitive to the single-base mismatches or abasic sites indicating the crucial importance of πstack mediated electrochemistry in the proposed detection scheme. The proposed approach, in conjunction with the spatial resolution of SECM and its ability to detect DNA hybridization opens new possibilities in the development of micro-array devices for DNA analysis.