The aim of this study was to evaluate the influenza vaccination status among paediatric patients with inflammatory bowel disease (IBD) in Poland. This was a questionnaire-based study. 242 patients with IBD and 142 controls were enrolled in the study. Of patients with IBD, 7·8% received an influenza vaccine, compared to 18·3% of controls (P = 0·0013). There were no statistically significant differences in time from IBD diagnosis, disease activity and in drugs, between vaccinated and non-vaccinated IBD children. In conclusion, the data of our study demonstrate an alarmingly poor influenza vaccination status in the majority of children with IBD. Therefore, there is an unmet need to implement better influenza vaccination strategies for this group of patients.