A deoxyribonuclease I (DNase I)-genotyping method using polymerase chain reaction (PCR) has been developed, underlying the molecular basis of the genetic polymorphism controlled by four codominant alleles, DNASE1*1, *2, *3 and *4. Two new alleles, DNASE1*5 and DNASE1*6, were recently discovered. In this study, we have added a new DNase I-genotyping method based upon both allele-specific amplification and mismatched PCR followed by Bam HI digestion. Using this method, the genotype distribution of DNase I in unrelated individuals from Shimane Prefecture in Japan was examined and compared with the results of other Japanese and/or ethnic population studies. The DNASE1 allele frequencies for the Japanese individuals from Shimane Prefecture were determined to be DNASE1*1 0.5763, DNASE1*2 0.4153 and DNASE1*4 0.0084 (X2=1.8304, 0.75> p >0.60). The existence of a decreasing north-to-south gradient in the DNASE1*2 allele was revealed from the study of 10 Japanese populations containing Shimane Prefecture. The allele frequency of DNASE1*2 of the Shimane Prefecture population was relatively lower than those of the German and Turkish populations but higher than that of the Ovambos population. These findings suggest the presence of a different mechanism in the chance fluctuaions of DNASE1 alleles among different populations.