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Despite the existence of international guidelines, vaccination in patients with inflammatory bowel disease (IBD) has not been integrated optimally. We developed a thorough education program, and compared its influence on vaccination rates with routine clinical practice in a tertiary IBD center.Between December 2014 and March 2015, we included 505 consecutive patients with IBD visiting our outpatient clinic (53% men, 72% Crohn's disease, median age 44 years). Vaccination data, including hepatitis B, influenza, pneumococcus, tetanus, and varicella zoster virus, as well as demographic data, were collected by a fellow in training or a certified gastroenterologist. Thereafter, patients were randomly assigned to group A receiving routine clinical practice or intervention group B receiving additional education by the IBD nurse with help of an information brochure and vaccination card. Vaccination status was reassessed 8 months later.At baseline, 32% of patients were vaccinated according to the guidelines. The remaining 346 patients were randomized to group A (n = 206) or intervention group B (n = 140). Eight months after randomization, 33% of intervention group B versus 6% of group A followed vaccination recommendations and differences were significant for each vaccine (all P < 0.001). A higher educational level was independently associated with better compliance to pneumococcal vaccination (P = 0.008) and to the guidelines overall (P < 0.001). However, the educational intervention was the only consistent factor independently associated with improved compliance to each individual vaccination recommendation (all P ≤ 0.023).Introduction of thorough vaccination education significantly increased compliance to vaccination guidelines. However, further education of patients and health care providers remains necessary.