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Aim: To describe the epidemiology, immunisation status and management of children with intussusception in the Northern Territory (NT), 1993-2003., Methods: Intussusception data were obtained from all NT hospitals using the International Classification of Diseases (ICD 9/10) codes for children under 18 years of age between 1993 and 2003. Medical records of these children were used to collect information on demographics, admission date, clinical symptoms, signs and management. Immunisation data were obtained from the NT immunisation register. The NT mortality database was reviewed for deaths from intussusception in children between 1993 and 2003. One death in an Aboriginal and Torres Strait Islander child was found in the NT mortality database. Medical records for this child were destroyed and so the case definition for intussusception used in this study was not fulfilled and the child was excluded., Results: Intussusception proven by radiological or surgical means was identified in 23 children from hospital records. The incidence for children with intussusception in NT is 0.65/1000 live births. The incidence of intussusception was lower in Aboriginal and Torres Strait Islander children (0.16/1000 live births) than in non-Aboriginal and Torres Strait Islander children (0.92/1000 live births) (P < 0.01)., Conclusion: The incidence of intussusception in the NT is similar to other developed countries but Aboriginal and Torres Strait Islander children have a very low incidence of intussusception. Intussusception is a rare event in the NT and will require a sensitive surveillance system to detect any potential increased risk of intussusception after the introduction of a new rotavirus vaccine.