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Coccidioidomycosis is often a self-limiting pulmonary infection, but it can cause more clinically apparent disease leading to hospitalization. We describe the characteristics of initial and subsequent hospitalizations in children with coccidioidomycosis.Using the Pediatric Health Information System (PHIS), an inpatient database, we identified retrospectively a cohort of patients hospitalized between April 1, 2002 and June 30, 2007 at children's hospitals across the United States. Demographic, clinical, and therapeutic data for the initial and subsequent hospitalizations were collected and analyzed.We identified 199 children who had 295 hospitalizations for coccidioidomycosis. The median hospital length of stay was 7 days (interquartile range: 3–14 days). Hospital incidence rates were stable from 2003 to 2005 but increased significantly from 2005 to 2006 (8.31/100,000 discharges vs. 12.95/100,000 discharges; χ2 = 4.65, P = 0.031). Fluconazole was the most commonly used antifungal agent, but 17.1% of patients were initially managed without antifungal therapy. The presence of an underlying comorbid condition was common (34.2%) as was the need for surgical intervention (41%). In-hospital mortality was low (1.5%).The increase in hospitalization rates associated with coccidioidomycosis from 2005 to 2006 mirrors the increase in cases reported to the Centers for Disease Control and Prevention during the same time period. Hospital admission for coccidioidomycosis seems to be more common in patients with underlying comorbid conditions and frequently necessitates surgical intervention.