A 10-year-old Japanese boy developed acute hepatitis with high levels of serum Torque teno virus DNA and marked lymphocytopenia, especially CD4 T-lymphocytopenia. Although the total lymphocyte counts rose as the patient recovered from hepatitis, this was largely because of a marked rise in CD8 cells. In contrast, CD4 cells recovered poorly, resulting in a further striking fall in the CD4/8 ratio. Two months later, the patient developed hepatitis-associated aplastic anemia. He was successfully treated with immunosuppressive therapy, which normalized the lymphocyte subset proportions. T-cell subsets analysis at the onset of hepatitis might be useful for predicting development of hepatitis-associated aplastic anemia.