The study of molecular markers to improve crops largely depends on the availability of rapid and efficient DNA extraction methods. Here we developed a cheap and convenient method to isolate genomic DNA from rice grains suitable for large-scale microsatellite analysis. We confirmed that the isolated rice DNA is suitable for PCR analysis with STS marker and SNP marker, as well as microsatellite marker. Further, we established high-throughput DNA extraction system in a 96-well plate format which make it possible high-throughput analysis of micro satellite markers with rice grains. This implies that the new method could be a useful tool for other types of marker analysis in large scale.