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Rotavirus is a leading cause of acute gastroenteritis among Taiwanese children. Two globally licensed rotavirus vaccines recommended for inclusion in routine immunization programs that have been available for private market use in Taiwan since 2006 have been associated with a low risk of intussusception in postmarketing studies conducted in several countries. Our objective was to examine trends and characteristics of intussusception hospitalizations in Taiwan among children <12 months of age before and after rotavirus vaccine licensure to provide updated baseline and early postlicensure data.We extracted data on intussusception-related hospitalizations among children <12 months of age during 2001–2013 from the National Health Insurance Research Database. We examined patient demographics, clinical outcome and hospitalization trends, focusing on recommended ages for rotavirus vaccination (6–14, 15–24 and 25–34 weeks). We compared mean hospitalization rates for prevaccine licensure years 2001–2005 with those for postvaccine licensure years 2007–2013 using Poisson regression analysis.During 2001–2013, 1998 intussusceptions hospitalizations were recorded. The mean age of hospitalization was 33 weeks. Almost all children recovered; 3 deaths occurred. The overall intussusception hospitalization rate was 75.1 per 100,000; seasonality was not evident. Hospitalization rates were greatest in children ≥25 weeks of age and occurred more frequently in boys. Prevaccine and postvaccine licensure trends in annual hospitalization rates did not significantly differ. However, mean hospitalization rates were lower during the postvaccine licensure period for children <12 months of age (rate ratio: 0.84, 95% confidence interval: 0.76–0.92) with the greatest decline among children 25–34 weeks of age (rate ratio: 0.66, 95% confidence interval: 0.55–0.78).Infant intussusception in Taiwan occurs at a rate within the range of other Asian countries is rare among children <3 months of age, has a male predominance and does not have a clear seasonality pattern. We did not observe a postlicensure increase in intussusception hospitalization rates in children 6–14 weeks of age.