In this study, to examine genetic variability within a breed and genetic relationships between populations/breeds, we genotyped 606 birds from seven Japanese native chicken breeds at seven polymorphic loci of egg white proteins and compared those with Asian native chicken populations and commercial breeds. Genotyping of the Japanese native breeds showed that ovalbumin, two ovoglobulins and ovotransferrin were polymorphic, but ovomacroglobulin, ovoflavoprotein and lysozyme were monomorphic. The proportion of polymorphic loci ($P_{poly}$) and average heterozygosity ($ar{H}$) within a population ranged from 0.286 to 0.429 and from 0.085 to 0.158, respectively. The coefficient of gene differentiation ($G_{ST}$) was 0.250 in the Japanese native chicken breeds. This estimate was higher than that of Asian native chicken populations ($G_{ST}$ = 0.083) and of commercial breeds ($G_{ST}$ = 0.169). Dendrogram and PCA plot showed that Satsuma-dori, Jitokko, Amakusa-daio and Hinai-dori were closely related to each other and grouped into Asian native chickens and that Tsushima-jidori, Nagoya and Chan (Utaichan) were ramified far from other Japanese native chicken breeds. The egg white protein polymorphisms demonstrated that the population differentiation of the seven Japanese native chicken breeds was relatively large.