PURPOSE: We previously reported that concurrent reactivation of latent Epstein-Barr virus (EBV) in children with hepatitis A virus (HAV) infection is common and EBV reactivation with HAV infection adversely affects the clinical features of hepatitis. However, the incidence of concurrent reactivation was not accurate because the detection of EBV reactivation was based on serologic methods. Therefore, we studied the effects of polymerase chain reaction (PCR)-proven EBV reactivation, thus a more precise concurrence, on acute HAV infection in children. METHODS: PCR were conducted in 34 patients, who had enrolled previous study and diagnosed with acute HAV infection between January 2008 and June 2010. Their medical records were reviewed. RESULTS: Among 34 patients with acute HAV infection, 12 patients (35.3%) had EBV reactivation which was proven using serologic and molecular biologic techniques. There were significant differences in the peak levels of AST and ALT between the reactivated and non-reactivated groups (p=0.001 and p<0.001, respectively). The duration of full recovery from hepatitis was more prolonged in the reactivated group (p<0.001). Clinical parameters, such as serum protein (p<0.001) and albumin concentrations (p<0.001), atypical lymphocyte count (p=0.001), prothrombin time-international normalized ratio (PT-INR, p<0.001), and splenomegaly (p<0.001), showed significant differences. The clinical features in the reactivated sub-group >10 years of age revealed more liver dysfunction compared to the non-reactivated sub-group. A comparison with a previous study was performed. CONCLUSION: PCR-proven reactivation of latent EBV in children with HAV infection is common and EBV reactivation with HAV infection adversely affects the clinical features of hepatitis, especially in older children.