Huntington's disease (HD) is associated with the expansion of a CAG repeat in the huntingtin gene. Molecular analysis of the repeat in Japanese HD patients and normal controls was performed. The size of the CAG repeat ranged from 37 to 95 repeats in affected subjects and from seven to 29 in normal controls. A significant correlation was found between the age of onset and the CAG expansion. The length of the expanded repeat is unstable in meiotic transmission and large increases occur in paternal transmission. At the same time the CCG repeat polymorphism adjacent to the CAG repeat was analysed and haplotypes of HD chromosomes were identified. Strong linkage disequilibrium was found between the CAG repeat expansion and an allele of (CCG)10 in Japanese HD chromosomes. It is distinct from that described previously in western populations. Western HD chromosomes strongly associate with an allele of (CCG)7. Possible mechanisms underlying the disequilibrium in Japan are discussed.