We designed a novel automated MagStation for high-throughput single nucleotide polymorphism (SNP) discrimination using dual-color hybridization. Magnetic particles (MPs) were used as target DNA carriers. The principle for SNP discrimination in this study was allele specific hybridization using dual-color fluorescent (Cy3, Cy5) probes. The MagStation is equipped with a 96-well automated magnetic separation unit which collects MPs on the side of the tubes as it moves to separation positions. The MagStation equips a heating block, where hybridization at different optimized temperature can be performed. This MagStation permits heating and magnetic separation of 96 samples per assay. The methylenetetrahydrofolate reductase (MTHFR) gene C677T polymorphism of 96 different samples was semi-automated integrated using this automated MagStation.