We have investigated a multiplex polymerase chain reaction (MPCR)-microchip electrophoresis (ME) method for the rapid detection of genetically modified organisms (GMOs) in soybeans. Using MPCR we amplified 100-bp DNA, which served as target DNA from a CaMV 35S promoter gene, which is contained in most GM-soybeans. The amplified 100-bp DNA fragment was separated in a conventional glass double-T microchip (100 mu m offset, 50 mu m wide and 20 mu m deep), based on gel electrophoretic separation, using a 0.5% poly(vinylpyrrolidone) (M-r 1,000,000) as a coating matrix, and 0.5% poly(ethyleneoxide) (M-r 8,000,000) as a sieving matrix. Under the electric field of 117.6 V/cm, the GM- soybean was analyzed within 80 s at the microchip. Compared to conventional slab gel electrophoresis, analysis time of the GM-soybean decreased approximately 20-fold, with excellent resolving power. The MPCR-ME technique may prove to be a new and effective tool for the analysis of GMO in grains and foodstuffs, due to its speed, simplicity, and high efficiency.