To investigate the relationship between atopy and hepatitis A virus (HAV) and hepatitis B virus (HBV) infections, we studied 42 children who had had HAV infection (Group I), 28 children who had had HBV infection (Group II), and 31 children who were seronegative for both HAV and HBV infection (Control group). Serological tests for HAV and HBV infections (anti-HAV IgG, HBsAg, anti-HBc IgG) and allergic skin tests and specific IgE investigations for the detection of atopy were carried out. In this study, there was no significant divergence in the socio-demographic characteristics among the three groups. The rates of specific IgE positivity in children in the HAV seropositive group (11.9%) and in children in the HBV seropositive group (17.8%) were lower than in the control group (35.4%) (p = 0.03 and p = 0.22, respectively). Also, the number of children with respiratory allergic diseases (allergic rhinitis and/or asthma) both in the HAV seropositive group and in the HBV seropositive group were significantly lower than in the control group (p < 0.05). When atopy in all of the groups was evaluated, the prevalence of atopy was found to be more widespread in HAV seronegative children (Adjusted OR, 9.2; 95% CI, 1.7-48.2) and HBV seronegative children (Adjusted OR, 5.9; 95% CI, 1.1-31.8) than in HAV and HBV seropositive children, after adjustment for age, number of older siblings and education of the father. In conclusion, in this study, the prevalence of atopy in children who had had HAV or HBV infection was found to be low, and this situation was considered to be related to the relationship of HAV and HBV infections to poor hygiene and to the fact that these infections occur at early ages in Turkey.