Nowadays, upper gastrointestinal endoscopy is very commonly performed procedure as a diagnostic tool or therapeutic purpose. Although perforation rate during diagnostic evaluation has been reported as low about 0.03%, gastrointestinal perforation is a critical problem to the patients owing to significant morbidity and hospital stay. Therefore, all endoscopists should know the risk factors for the perforation and pay attention to avoid this complication. We experienced a case of 66 year-old-male with duodenal microperforation after endoscopic biopsy. During endoscopic examination, a submucosal mass was detected at duodenal second portion and endoscopic biopsy was performed. After this, he complained of severe abdominal pain during colonoscopy. Emergent simple abdomen and abdominal computed tomography revealed multiple free air in retroperitoneal space and duodenal perforation was suspicious. He was treated with primary closure and then recovered completely. Therefore, we report a case with microperforation after endoscopic duodenal biopsy.