Primary invasive aspergillosis of the gut is a rare event and is associated with high mortality. We report for the first time on a patient who had isolated aspergillosis of the small bowel after autologous stem cell transplantation. Diagnosis of invasive aspergillosis of the gut was based on abdominal pain, galactomannan antigenemia and isolation of Aspergillus fumigatus from the stool and was later confirmed by pathohistologic examination. No other site of invasive aspergillosis was evident. The patient was successfully treated with early surgery and combination antifungal therapy.