In spite of the fact that pouchitis is the most frequently occurring and troublesome complication found in patients treated by ileo-anal anastomosis for ulcerative colitis, no biological marker currently exists to monitor the outcome of the disease. Since it has been noted faecal butyrate is reduced in patients with pouchitis, we developed a simple gas chromatography method to quantify butyrate in faecal water. This test is based on diethyl ether extraction with the use of methacrylic acid as an internal standard. We demonstrated that butyrate was effectively measured when this technique was applied to eleven patients with ileal-pouch anal anastomosis within the first year after the closure of their ileostomy. We also observed a noticeable reduction in the concentration of butyrate in patients who went on to develop a pouchitis.