Streptococcus pneumoniae is a major cause of pneumonia and sinusitis. Pneumonia kills >1 million children annually, and sinusitis is a potentially serious pediatric disease that increases the risk of orbital and intracranial complications. Although pneumococcal conjugate vaccine (PCV) is effective against invasive pneumococcal disease, its effectiveness against pneumonia is less consistent, and its effect on sinusitis is not known. We compared hospitalization rates due to sinusitis, pneumonia, and empyema before and after sequential introduction of PCV7 and PCV13.