In the summer of 2003 in Jerusalem, Israel, 23 children were hospitalized with influenza A virus (A/Fujian/411/02-like virus) infection. The majority were neonates and infants. Clinical manifestations included neonatal fever, bronchitis, bronchiolitis, and pneumonia, and outcomes were favorable. Continued surveillance between epidemic seasons could allow early recognition of influenza strains that will appear in the following influenza season.