The known intestinal complications of systemic sclerosis (SSc) stem mainly from motor disturbances. Autopsy findings were studied to identify anatomic abnormalities that may be associated with this disease. Descriptions of intestinal organs at autopsy were compared in 16 patients with SSc and 18 patients with systemic lupus erythematosus (SLE), a related disease control. There was a high incidence of perforation in SSc (7 of 16 patients) compared to SLE (1 of 18 patients) (P < 0.05). In SSc, perforations involved all parts of the bowel: transmural esophageal fibrosis (after heater probe cautery), dehiscence of suture line after gastric resection, perforated duodenal ulcers (N = 2), terminal ileal ischemia, and diverticulitis (N = 2). Two of the perforations in SSc were silent and were discovered at autopsy. The one perforation in SLE was due to full-thickness necrosis from vasculitis. This study suggests that the intestinal walls of patients with SSc are inherently weak; the gastroenterologist should keep this in mind when performing invasive procedures.