BACKGROUND: Intussusception, a condition where one segment of intestine invaginates into another, occurs predominantly in infants and young children. A number of potential causes have been identified including infectious agents and rotavirus vaccination. Following the introduction of rotavirus vaccination of infants in Western Australia, a laboratory surveillance programme testing notified intussusception cases for infectious agents was commenced. This led to a PCR-based study of the association between gastrointestinal viruses and intussusception. OBJECTIVES: Conduct viral testing on stool samples from intussusception patients to determine viruses that may have an association with intussusception. STUDY DESIGN: A retrospective case-control study was conducted using stool samples collected from children with intussusception (n=74) and matched controls (n=289) between 2008 and 2011. Samples were tested for rotavirus, norovirus, adenovirus, enterovirus, rhinovirus, astrovirus, parechovirus and bocavirus. Adenovirus, enterovirus and rhinovirus species were determined by DNA sequencing. RESULTS: Human adenovirus C was detected in significantly more cases than controls with 31/74 (41.9%) cases testing positive compared to 39/289 (13.49%) controls (OR=4.38, p<0.001). A significant difference was seen in Enterovirus B detections with 11/74 (14.9%) cases testing positive compared to 21/289 (7.3%) controls (OR=2.24, p=0.04). Rotavirus was detected in 7/74 (9.46%) cases and 11/289 (3.81%) controls, which was also a significant difference (OR=2.88, p=0.045). CONCLUSIONS: Our results show that intussusception is associated with non-enteric adenovirus infections, and Enterovirus B infections. While a statistical association was seen with rotavirus and intussusception, we were not able to determine if this was related to vaccine strain or wild type rotavirus.