This study aimed to document the baseline incidence and epidemiology of intussusception (IS) in Malaysia. This retrospective surveillance examined hospital discharge data from three hospitals in Malaysia to identify IS cases over a 3-year period (2000-2003) in children <5 years of age. Identification of definite cases of IS was done through a search of computerized hospital discharge records (ICD-9-CM code 560.0) followed by confirmation of diagnosis through medical record review. The definition of IS was based on the clinical guidelines from the IS Brighton Collaboration Working Group, version 2002. During the 3-year study period, there were 62 cases hospitalized due to IS, of which 74.2% were < 1 year of age. The incidences for hospitalization due to IS in children < 1 year old and < 5 years old averaged 17.8 and 4.8 per 100,000 person-years, respectively. No IS-associated deaths were recorded and all IS cases had a favorable outcome. No distinct seasonality with IS occurrence was observed.