From 1996 to 2009, we analyzed changes in pneumococcal disease (PD) in Utah children aged <18 years using International Classification of Diseases, ninth revision coded hospital discharges. We observed a sustained decrease in the incidence of PD among children <5 years in 2001–2004 (−36%) and 2005–2009 (−34%) compared with 1996–2000 (pre-7-valent pneumococcal conjugate vaccine). Decreases were primarily in bacteremia, uncomplicated pneumonia, and meningitis. In contrast, significant increases in complicated pneumonia/empyema were noted in children <5 years (+95% and +85%) and 5 to 17 years (+2% and +70%). Despite decreases in PD among Utah children, complicated pneumonia/empyema has increased during the 7-valent pneumococcal conjugate vaccine era.