Incidence of Kawasaki disease (KD) varies geographically, with highest rates in East Asia and comparatively lower rates in Europe and United States. Population-based epidemiologic studies of KD in Latin American countries have not been done. The purpose of this study is to determine demographic characteristics, hospitalization rates and estimated incidence of KD in Chile. We performed a retrospective review of national hospital discharge databases between 2001 and 2007 for patients younger than 18 years of age with KD (ICD10 code M30.3). Seven hundred and eighty-six hospitalizations with discharge diagnosis of KD were identified, representing 0.03% of hospitalizations. Median age of diagnosis was 1 year, and 85% of patients were younger than 5 years. Male-to-female ratio was 1.6:1. Highest hospitalization rates occurred in late winter/spring (August-November) with a smaller peak in summer (March). KD-associated hospitalization rate was 7.6 per 100,000 children younger than 5 years (95% CI 7.0-8.1). Hospitalization rates increased 47% between 2001-2004 and 2005-2007 periods: 6.3 (95% CI 5.6-7.0) to 9.3 (95% CI 8.3-10.3), (P < 0.001). Estimated incidence of KD, assuming 10% readmission rates, was 6.8 (95% CI 6.3-7.4), increasing from 5.7 (95% CI 5.0-6.3) in 2001-2004 to 8.4 (95% CI 7.4-9.3) in 2005-2007 (P < 0.001). In conclusion, demographic characteristics of Chilean patients with KD are similar to international data. There has been an increase in hospitalization rates and estimated incidence of KD in Chile between 2001 and 2007. This may reflect a true increase in cases or improved awareness.