Studies involving human intestinal tissue are essential for advancing the field of celiac disease (CeD), as diagnosis requires duodenal biopsies. Performing studies in children helps to better understand CeD in this important subpopulation. This study aims to determine the risk in obtaining duodenal research biopsies during pediatric endoscopy. In this retrospective chart review from 2016 to 2022 of 1180 research subjects and controls, there were 18 procedure-related adverse events within 48 hours. Most adverse events were for symptoms of pain and fever. There was no increased risk of adverse events if additional duodenal research biopsies were taken during pediatric endoscopy.