Background: hepatitis E virus (HEV) and hepatitis A virus (HAV) are acute hepatitis that infects mainly children. They are feco-orally transmitted disease. Objectives: detection of the prevalence of HAV and HEV in children with acute hepatitis and their correlation with the immune response. Methodology: 151 hepatic children from Children's Hospital in Assiut were enrolled in our study. Anti-HEV IgM, anti-HAV IgM, liver function tests and the immune response using Flow Cytometry measuring CD4+CD25+Foxp3 and intracellular IL-10 were measured. Results: in anti HAV-IgM patients, 66.36 % were males and 33.64 % were females, 42.72 % were urban and 57.28 % were rural, while in HEV-IgM positive patients 57.14 % were males and 42.86 % were females. 42.86 % were urban and 57.14 % were rural, the level of CD4+CD25+Foxp3 was statistically significant (P=0.027), and IL-10 was statistically significant (P=0.007). Conclusion: there was a significant correlation between the presence of the viruses and the immune response.