Intussusception is the most common cause of intestinal obstruction in young children. The pathogenesis of intussusception is still not well understood. In this study the pathogens from stool specimens were investigated in children with intussusception. Patients diagnosed with primary idiopathic intussusception were enrolled. Pathogenic bacteria and viruses were detected in the stool samples by routine culture, cell culture, polymerase chain reaction, reverse transcriptase-polymerase chain reaction, enzyme immunoassay, and electron microscopy examinations. A total of 71 samples were analyzed during the 2-year study period. The patients ranged in age from 4 to 47 months. Viruses were detected in 56 of the 71 stool samples (78.9%). Adenovirus was found in 19 of 35 cases aged <2 years, whereas it was found in 17 of 21 cases aged ≥2 years. The majority of adenovirus isolates were non-enteric organisms generally associated with respiratory tract symptoms. These results suggest a casual association of viral infections in children with intussusception. Adenovirus infection, especially with the primary non-enteric types, is a significant risk factor for developing intussusception in children, particularly those aged over 2 years.