It is recommended to investigate the serology of hepatitis B virus (HBV) and vaccinate seronegative patients at the time of diagnosis in inflammatory bowel diseases (IBD). This study aimed to investigate the efficacy of HBV vaccine and factors affecting the response.In this retrospective, observational study, HBV-seronegative IBD patients were administered 3 doses (at months 0, 1, and 6) recombinant 20 μg HbsAg. Patients' demographics, IBD attributes, and treatment methods were investigated as the factors with potential impacts on vaccination outcomes.One hundred twenty-five patients with IBD were evaluated. The number of patients with Anti-HBs >10 IU/L was 71 (56.8%), and the number of patients with anti-HBs >100 IU/L was 50 (40%). Age, disease activity, Crohn disease subtype, and immunosuppressive treatment (IST) were found to have significant effects on immune response (P = 0.011, P < 0.001, P = 0.003, and P < 0.001, respectively). With multivariate analysis, age < 45 years (OR 3.1, 95% CI 1.2-8.3, P = 0.020), vaccination during remission (OR 5.6, 95% CI 2.3-14, P < 0.001), and non-IST (OR 11.1, 95% CI 2.9-43.2, P = 0.001) had favorable effects on the occurrence of adequate vaccine response.The likelihood of achieving adequate immune response with standard HBV vaccination protocol in IBD is low. Selecting vaccination protocols with more potent immunogenicity is a better approach to achieve effective vaccine response in patients with multiple unfavorable factors.