Nucleic-acid hybridization assays based on the use of different inorganic-colloid (quantum dots) nanocrystal tracers for the simultaneous electrochemical measurements of multiple DNA targets are described. Three encoding nanoparticles (zinc sulfide, cadmium sulfide, and lead sulfide) are used to differentiate the signals of three DNA targets in connection to stripping-voltammetric measurements of the heavy metal dissolution products. These products yield well-defined and resolved stripping peaks at -1.12 V (Zn), -0.68 V (Cd), and -0.53 V (Pb) at the mercury-coated glassy-carbon electrode (vs Ag/AgCl reference). The position and size of these peaks reflect the identity and level of the corresponding DNA target. The multi-target detection capability is coupled to the amplification feature of stripping voltammetry (to yield femtomole detection limits) and with an efficient magnetic removal of nonhybridized nucleic acids to offer high sensitivity and selectivity. The protocol is illustrated for the simultaneous detection of three DNA sequences related to the BCRA1 breast-cancer gene in a single sample in connection to magnetic beads bearing the corresponding oligonucleotide probes. The new electrochemical coding is expected to bring new capabilities for DNA diagnostics, and for bioanalysis, in general.