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The aim of the study was to evaluate the response to hepatitis A and B vaccinations in pediatric patients with celiac disease (CD).Thirty patients with CD ages 1 to 15 years were compared with 50 healthy age-, sex-, and body mass index–matched controls. Screening for hepatitis A and B serology was carried out before vaccination. Susceptible cases received 20 μg of recombinant DNA vaccine for hepatitis B (0,1, and 6 months) and 720 milliELISA units of inactivated hepatitis A virus (HAV) vaccine (0 and 6 months). Postvaccination serologic evaluation was performed 1 month after the last dose of primary vaccination, 1 month after the booster dose, and once every year during follow-up.Sixteen patients and 35 controls received hepatitis A vaccine; protective anti-HAV antibodies were developed in 12 (75%) of the patients and all of the controls (75% vs 100%, respectively; 95% confidence interval [CI] 0.47–0.92, P = 0.007). Thirty patients and 50 controls received hepatitis B vaccine, and 70% of the patients vs 90% of the controls achieved seroprotection (anti-HBs titers ≥10 mIU/mL) 1 month after primary vaccination (95% CI 0.74–0.90, P = 0.03). Four patients were unresponsive to both of the vaccines. The overall seroprotection rates were 96% in controls and 80% in patients after the whole hepatitis B vaccination series (95% CI 0.04–0.18, P = 0.04). No significant reduction was observed in antibody response among patients and controls during follow-up period.The rate of seroconversion to the hepatitis B virus- and HAV vaccine is lower in patients with CD than in healthy controls.