A novel, rapid, and sensitive protocol for the electrochemical detection of DNA hybridization that take the advantage of a magnetic separation/mixing process and the use of monomaleimido-gold nanoparticles of 1.4 nm diameter as label is presented. A sandwich-type assay is formed in this protocol by the capture probe DNA immobilized on the surface of magnetic beads and the double hybridization of the target (cystic fibrosis related DNA), first with the immobilized probe, and then with signaling probe DNA labeled with monomaleimido-gold nanoparticles. When the assay is completed, the final conjugate is transferred onto genomagnetic sensor surface (graphite epoxy composite electrode with a magnet inside) used as working electrode, and then the direct determination of gold nanoparticles by differential pulse voltammetry striping technique is carried out. This protocol is quite promising for numerous applications in different fields as clinical analysis, environmental control as well as other applications.