- Background and Aims: Response rate to second-generation hepatitis B virus vaccines is relatively low in patients with inflammatory bowel diseases compared with the general healthy population. We compared the efficacy and safety of a third- vs a second-generation hepatitis B virus vaccine in a group of patients with inflammatory bowel diseases treated with immunosuppressive medications. Methods: Prospective, randomised, single-blind, controlled study. Eligible patients were randomly assigned to receive one of two vaccines, ENGERIX-B or Sci-B-Vac. The vaccines were administered in three doses at 0, 1, and 6 months. The primary endpoint was defined as the titre of anti-hepatitis B S [HBs] antibodies following the standard three-dose hepatitis B virus vaccination schedule. Results: A total of 72 patients complied with study protocol [37 and 35 patients in the ENGERIX-B and Sci-B-Vac groups, respectively]. Overall, 75% of the cohort seroconverted. The primary endpoint was met in 81.1% in the ENGERIX-B group and 68.6% in the Sci-B-Vac group [ p = 0.22]. Patients in the Sci-B-Vac group showed a statistically significant decreased seroconversion rate compared with the ENGERIX-B group, with use of tumour necrosis factor [TNF] alpha inhibitors [ p = 0.03], and higher degree of disease activity [ p = 0.03]. Conclusions: Overall seroconversion rate in our cohort was higher than in previous reports in the literature, possibly due to a low disease activity state in the majority of participants. Third-generation hepatitis B virus vaccines showed no apparent advantage over standard of care vaccine in this patient group.