OBJECTIVE To analyze the clinical characteristics of acute kidney injury (AKI) in critically ill childhood patients with influenza A virus (H1N1) and enterovirus 71 (EV71), and to study the significance of the serum creatinine and urine output in diagnosis of AKI. METHODS The clinical data of AKI in critically ill children admitted to intensive care units (ICUs) with confirmed influenza A (H1N1) or enterovirus 71 infection (EV71 group) from Oct. 2009 to Oct. 2010. RESULTS Twenty-eight critically ill children were involved in the study. In H1N1 group, there were 18 cases including 6 males and 12 females, and the average age was 5.4 years. In EV71 group, there were 10 cases including 8 males and 2 females, and the average age was 1.1 years. In H1N1 group: 4 cases developed AKI, whose average number of involved organ was 5.3. Two children were classified as first stage completely recovered after treatment; three children who were classified as third stage died. In 14 children without AKI, the average number of involved organ was 3.0, four of these children died. In EV71 group: 3 cases (first stage) developed AKI and 3 cases' serum creatinine increased to 45.0 to 47.6 percent from baseline. The average number of involved organ was 5.7. All the six children died. The other 4 cases whose serum creatinine was normal, and the average number of involved organ was 3.0, recovered. CONCLUSIONS In critically ill virus-infected children, more organs were involved in the patients who developed AKI. As to influenza A (H1N1) infected critically ill children, the prognosis was comparatively better if the children were classified as AKI stage 1 and received early effective treatment. On the contrary, the prognosis was comparatively worse for those with AKI stage 3. As to EV71 infected critically ill children, the prognosis was worse once AKI developed. As to diagnosis of AKI, the sensitivity of serum creatinine criteria seemed to be superior to the urine output criteria. However, the significance of the serum creatinine and urine output in diagnosis of AKI still needs to be investigated in the future in large scale clinical studies.