We report a case of a gastrointestinal stromal tumor (GIST) with strong and faint KIT protein staining, respectively, at two different sites. A single point mutation (c1727 T>C) was detected in DNA extracted from both sites, and a further deletion mutation (c1678_1680 del GTT) was detected in DNA from the site with strong KIT protein staining. Cloning analysis indicated that the point mutation and the deletion were present on different alleles.