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Pediatric patients with inflammatory bowel disease are undervaccinated against influenza. Gastroenterology nurses are ideally situated to assist in improving vaccination in this population. The objective of this quality improvement project was to evaluate the implementation of information technology prompts within the electronic medical record to improve influenza vaccination during specialty clinic visits. The proportion of patients with yearly influenza vaccination was evaluated at baseline, Year 1, and Year 2 following implementation. At baseline, only 10% of a random sample had documented influenza vaccination. Vaccination documentation improved to 39% (96/246) by Year 1 and to 61% (175/287) by Year 2 (p < .001). Vaccine counseling improved from 27% to 77% by Year 2 for unvaccinated patients (p < .001). Among patients seen by gastroenterology nurses, the proportion of patients with either documented vaccination or counseling was 94% by Year 2 compared with 70% if seen only by a physician (p < .001). Documentation of influenza vaccination improved with the use of customized prompts. Patients seen by a gastroenterology nurse had higher vaccination documentation and vaccine counseling than those who were seen by a physician alone.