Gastrointestinal stromal tumors (GISTs) are the most common gastrointestinal mesenchymal tumors driven by KIT or PDGFRA mutations. A majority of these mutations affect KIT exon 11 and represent deletions or point mutations, but insertions and duplications have also been reported. The latter have been found exclusively in the 3' part of KIT exon 11. Reported frequency of duplications varies, and a higher frequency has been reported in studies based on frozen tissue. Recently, we have hypothesized that in some cases, the duplications might remain undetected in formalin-fixed, paraffin-embedded GISTs because of the preferential polymerase chain reaction (PCR) amplification of wild-type KIT over the mutant allele. In this study, 16 GISTs initially diagnosed as a wild-type KIT were evaluated using PCR assay amplifying only the 3' part of KIT exon 11, the region commonly affected by duplications. Denaturing high-pressure liquid chromatography and direct sequencing analyses revealed duplications in 4 (25%) of 16 analyzed cases. Use of the PCR assay amplifying the specific region affected by duplications and yielding 129 bp in wild-type KIT can substantially improve the detection of these mutations in formalin-fixed, paraffin-embedded GISTs.