We attempted to predict epidemics of influenza B, focusing on B/Victoria/2/87-like (V) and B/Yamagata/16/88-like (Y) lineages, in Yamagata, Japan. We collected 9624 nasopharyngeal swabs for virus isolation from patients with respiratory infections between 1996 and 2003 and 237 sera for seroepidemiological analysis by haemagglutination–inhibition test in 2001. We isolated 424 V-lineage and 246 Y-lineage viruses during the study period. Three herald viruses in the 2000–2001 season enabled us to predict a V-lineage epidemic in the following season. However, another V-lineage epidemic occurred in the 2002–2003 season, although we caught four herald Y-lineage viruses, whose antigenic drift was suggested by seroepidemiological study, at the end of the previous season. Since the epidemiology of the two influenza B lineages remains unclear, a careful watch should be kept on these lineages in order to provide effective public-health strategies against future epidemics.