Five hundred eighty-seven adenovirus type 3 (Ad3) isolates were established from children with acute respiratory infections (ARI) from 1986 to 1991, in Yamagata, Japan. Ad3 could be found in almost all the months during the 6 years when two epidemics occurred, in 1987 and 1989. A molecular epidemiological study was done on 346 of the 587 isolates, using restriction endonucleases; BamHI, HindIII, SmaI, and BgIII were used. The Ad3 isolates were classified into seven genome types. The genetic differences among the seven genome types were < 0.9%, and their phylogenetic tree, estimated by the neighbor-joining method, correlated highly with their monthly distribution. One genome type predominated for 56 months, while the other six related genome types cocirculated for a short period. These results suggested that the predominant genome type of Ad3 might have been endemically perpetuated in the Yamagata area with minor genomic variations. Furthermore, the outbreaks of Ad3 may have been due not to the appearance of a new genome type but rather to the endemic genome type.