Peritonitis is a serious problem in patients undergoing peritoneal dialysis. Rarely pneumatosis intestinalis can occur as a complication of this infectious process. Pneumatosis intestinalis is a potential life threatening condition with a challenging management. The mortality of peritoneal dialysis patients with pneumalosis intestinalis secondary to mesenteric ischemia is almost 100%. We describe a rare case of pneumatosis intestinalis in a peritoneal dialysis patient who developed Staphylococcus aureus peritonitis which was initially treated with appropriate antibiotics. Since initial response to therapy was not achieved, an abdominal computerized tomography was done which revealed a pneumatosis intestinalis. A laparotomy was performed and small bowel necrosis was seen. A segmental resection with ileostomy, jejunostomy was done. Though surgical treatment was performed, the patient died in 2 weeks after admission. Pneumocystitis intestinalis in peritoneal dialysis peritonitis is a uncommon complication which requires prompt evaluation to rule out mesenteric ischemia as it carries a high mortality and its management will be surgical.