A 32-year-old overweight asymptomatic man was found to have a persistently raised serum alkaline phosphatase at 250–300 U/l (normal range <130). Other liver function tests were unremarkable apart from an initial marginally elevated alanine transaminase, which normalised with weight reduction. Abdominal imaging revealed a fatty liver but an extensive serological search for significant hepatobiliary disease was negative. Subsequent isoenzyme electrophoresis revealed normal liver and bone fractions of alkaline phosphatase but a grossly elevated intestinal fraction. Elevated intestinal fraction of alkaline phosphatase should be considered in the investigation of unexplained alkaline phosphatase, particularly when the usual associated hepatobiliary and bony pathologies are not present. Although an elevated intestinal fraction of alkaline phosphatase can be linked to significant gastrointestinal pathology, this case report highlights that it can be a benign biochemical finding.