AimThere are few data regarding the safety and effectiveness of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) vaccines in patients with intractable hepatobiliary diseases. We conducted a multicenter, questionnaire‐based, cross‐sectional study to determine the safety and effectiveness of the SARS‐CoV‐2 vaccines in Japanese patients with intractable hepatobiliary disease.MethodsPatients aged ≥18 years with autoimmune hepatitis (AIH), primary biliary cholangitis, primary sclerosing cholangitis, Budd–Chiari syndrome, idiopathic portal hypertension, and extrahepatic portal vein obstruction at each center were consecutively invited to join the study. Participants were asked to complete a questionnaire regarding their characteristics, vaccination status, post‐vaccination adverse effects, and SARS‐CoV‐2 infection. Additionally, liver disease status, treatment regimens, and liver function test values pre‐ and post‐vaccination were collected.ResultsThe survey was conducted from September 2021 to May 2022, and 528 patients (220 AIH, 251 primary biliary cholangitis, 6 AIH– primary biliary cholangitis/primary sclerosing cholangitis overlap, 39 primary sclerosing cholangitis, 4 Budd–Chiari syndrome, 5 idiopathic portal hypertension, and 3 extrahepatic portal vein obstruction) participated in the study. Post‐vaccination adverse effects were comparable to those observed in the general population. Post‐vaccination liver injuries classified as grade 1 or higher were observed in 83 cases (16%), whereas grades 2 and 3 were observed in only six cases (1.1%); AIH‐like liver injury requiring treatment was not observed. Overall, 12 patients (2.3%) were infected with SARS‐CoV‐2, and only one patient was infected 6 months after the second vaccination.ConclusionSARS‐CoV‐2 vaccines demonstrated satisfactory safety and effectiveness in Japanese patients with intractable hepatobiliary diseases.