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Aim of the study was to evaluate the response to hepatitis A and B vaccination in pediatric patients with inflammatory bowel disease (IBD).A total of 47 patients with IBD (25 ulcerative colitis, 14 Crohn disease, and 8 indeterminate colitis) ages 3 to 17 years were compared with 50 healthy age- and sex-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 vaccine (HAV) (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.A total of 23 patients and 35 controls received HAV and protective anti-HAV antibodies were developed in all of the patients and controls (P = 1.00). Forty-seven patients and 50 controls received hepatitis B vaccine and 70.2% of the patients versus 90% of the controls achieved seroprotection (anti-HBs titers ≥10 mIU/mL) 1 month after primary vaccination (95% confidence interval 0.71–0.87, P = 0.02). The overall seroprotection rates were 96% in controls and 85.1% in patients after the whole hepatitis B vaccination series (95% confidence interval 0.83–0.95, P = 0.08). No significant reduction was observed in antibody response among patients and controls during the follow-up period.The rate of seroconversion to the hepatitis B vaccine was lower in pediatric patients with IBD than in healthy controls and hepatitis A vaccine was highly immunogenic among patients with IBD.