In familial adenomatous polyposis (FAP), inactivation of the APC gene is directly linked to the development of gastrointestinal polyps and cancer. It is likely that other epigenetic factors are involved in the malignant change of polyp to carcinoma. Previous studies have implied an abnormal bile acid profile, both in faeces and bile. In this study, using carefully matched control groups, extraction of bile acids from faeces and bile was performed and analysis was rigorously performed using Gas-liquid chromatography-Mass Spectrometry. No significant differences were found between the two groups in the profile of major bile acids. An increased faecal excretion of two minor bile acids, 5β-cholanoic acid-3α-ol-12-one and 5α-cholanoic acid-3α-ol-12-one and an increased level of 5β-cholanoic acid-3α-01-12-one in bile was found in patients with FAP. A difference in the faecal neutral sterol profile had also been suggested, but this study showed no significant difference between the two groups when matching controls are used. This study does not support the idea that there are significant differences in faecal bile acid, biliary bile acid or neutral sterol profiles between individuals with familial adenomatous polyposis and controls.