Fluorescence polarization technique can specifically detect nucleotide sequences by hybridization without separation procedures. We applied the technique to the detection of the Shiga toxin genes ( stx 1and stx 2) in enterohemorragic Escherichia coli (STEC). STEC possesses stx 1 and/or stx 2 and using MK primers, the amplification of stx 1 and/or stx 2 can be performed universally, but the band sizes for both genes are almost identical; thus the genotype is hard to determine using electrophoresis. To identify stx genotype, conventional PCR combined with electrophoresis requires a second amplification process with more than 25 temperature cycles using other genotype-specific primer pairs. However, using the newly developed method only a few temperature cycles of the asymmetric PCR using the same MK primers and two different probes for stx 1and stx 2 were needed. The incubation time for probe hybridization was 10 minutes, and the detection time for fluorescence polarization was within about 1 minute per sample. Thus, we considered that the detection method using fluorescence polarization technique was a rapid and reliable method for detecting stx 1and/or stx 2.