To date, there has been no report of co-infection of chicken anemia virus (CAV) with enteric virus in patients with acute gastroenteritis (AGE). CAV has been recently detected in various types of human samples including stool, indicating pathogenicity in gastrointestinal tract. Examination by PCR-based methods of CAV and norovivus genogroup II (NV GII) in stool of 110 children with AGE at a hospital in Taiwan revealed for the first time of co-infection in two cases. This is the first description of CAV infection in children with AGE in Taiwan. Systematic surveillance and evidence-based studies are required to determine the transmission pathways and spread of CAV in Taiwan.