The polymorphism of the Sec2 gene, which determines Se blood type, has been reported. This study presents an Se genotyping system by the allele-specific polymerase chain reaction amplification method. The Se, sej and se(fus) alleles were amplified using allele-specific primers. The Sec1, Sec2 and se(fus) genes were analyzed by DNA sequencing. The 299-bp Se, 146-bp sej and/or 312-bp se(fus) allele-specific products were amplified and detected in the native polyacrylamide gel. The 314th-316th nucleotides of the Sec1 gene were CCC, which were different from the nucleotides GGG reported previously by Kelly et al. [J Biol Chem 270 (1995) 4640]. This Se genotyping system is a simple method available for the forensic science field in Japan. The crossover region of the se(fus) gene is a 164-bp stretch corresponding to the regions between the 253rd and 416th of the Sec1 gene and between the 211th and 374th of the Sec2 gene.