Abstract Background Colonic ischaemia is a well documented complication of abdominal aortic reconstruction. In this prospective study patients had routine preoperative and postoperative colonoscopy and biopsy, in order to determine the true incidence and implications. Methods Fifty-six patients undergoing elective infrarenal aortic surgery, 28 for aneurysm and 28 for occlusive disease, had colonoscopy and biopsy before and 1 week after operation. Results Colonic ischaemia was identified histologically in biopsies from 16 (30 per cent) of 53 patients. Almost half the patients had normal macroscopic appearances. Two factors exhibited a statistically significant association with the development of ischaemia: prolonged cross-clamp time (P < 0·05) and postoperative diarrhoea (P < 0·001). Co-morbidity was much higher in patients with colonic ischaemia (P < 0·005). Overall morbidity was significantly greater in the aneurysm group (P < 0·05). Conclusion Colonic ischaemia is common after aortic reconstruction. When suspected, colonoscopy with biopsy is diagnostic.