The osteogenic differentiation of mesenchymal stem cells (MSCs) was assessed by determining the gene expression levels of proteins; osteocalcin (OSC), osteonectin (OSN) and osteopontin (OSP) based on electrochemical detection protocol combined with genomagnetic assay in parallel to real-time PCR analysis. Genomagnetic assay was performed using streptavidin coated commercial magnetic particles (magnetic beads, MBs) in combination with single-use electrochemical sensor technology. A biotinylated DNA probe was immobilized onto streptavidin coated magnetic particles, and then the hybridization process of the probe with its complementary DNA was performed. The oxidation signals of DNA electroactive bases guanine and adenine were measured voltammetrically using a pencil graphite electrode (PGE) before and after the hybridization process of OSC/OSN/OSP probe sequences with their complementary target sequences. The selectivity of the genomagnetic assay was also tested using each DNA probe individually related to osteogenic differentiations. The voltammetric detection of osteogenic differentiations was confirmed selectively by real-time PCR analysis.