Background: Colonic injury represents a rare complication of percutaneous nephrolithotomy (PCNL). Injury of the small bowel is very rare, with only anecdotal case reports in the literature. We report here a rare PCNL complication of jejunal perforation without concomitant colonic injury. Case Presentation: A 45-year-old male underwent PCNL for multiple left kidney stones. At the beginning of the procedure, we faced difficulty in achieving access, but after that the procedure was straightforward and ended smoothly. However, from the third day, the postoperative course became stormy with progressive development of picture of acute peritonitis. Laparotomy was mandatory and jejunal perforation was found and repaired. Conclusion: Although extremely rare, small bowel injury should be kept in mind during planning for percutaneous nephrolithotomy. Prompt diagnosis and active treatment should be undertaken without delay especially if picture of acute peritonitis is developed.