This study was designed to determine the clinical characteristics of children infected with different strains of influenza B viruses isolated in southern Taiwan. The clinical features were compared with influenza A infection occurring in the same period. All children enrolled in the study had laboratory-confirmed infection with influenza A or B viruses. Influenza B speciation was performed by RNA extraction, cDNA synthesis, and amplification by polymerase chain reaction and sequencing. Demographic data, clinical findings, diagnoses, and outcomes were obtained. During the study period, 163 strains of influenza A and 118 strains of influenza B were isolated. The Yamagata-like strains were most prevalent in 2001. New reassortant strains were identified since 2002 and became predominant in 2005 and 2006. Children with influenza B were more likely than those with influenza A to be diagnosed as upper respiratory tract infection, myositis, and gastroenteritis (P < 0.05). Children infected with Yamagata-like strains were more likely to develop lower respiratory tract infection (P < 0.05) and accounted for all cases of invasive disease. Children infected with the Victoria-like group had the longest hospital stays associated with severe bacterial superinfection. Currently new reassortant influenza B viruses are the predominant strains circulating in southern Taiwan. There is considerable similarity of clinical features between influenza A and B in children. The Yamagata-like strains were associated with more invasive infections. Continuous influenza virus surveillance is essential particularly in Taiwan where pandemic strains tend to appear earlier than in other countries.