We identified two novel dinucleotide polymorphisms in intron A at nucleotide 192 (FIX192) and in the 5' flanking region at nucleotide -793 (FIX-793) of the factor IX gene, which are present in normal Japanese. The Hha I restriction fragment length polymorphism (FIX-HhaI) located 8 kb 3' to the factor IX gene was also found to be an efficient marker for detecting carriers in a Japanese family with hemophilia B. Each of these polymorphisms was able to be rapidly ascertained by the polymerase chain reaction (PCR) technique. In 22 Japanese families with hemophilia B, 18 families (81.8%) were heterozygous for at least one of these polymorphisms, whereas 11 (50%) were informative for the extragenic DXS99/Sac I RFLP which was previously reported as a useful gene marker for Japanese hemophilia B. Using all 4 polymorphisms together, the informative rate improved to 86.4%. Carrier detection and, possibly, the prenatal diagnosis of hemophilia B can be achieved effectively and rapidly in Japanese with these polymorphisms.