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Gastrointestinal stromal tumours (GIST) are the most common mesenchymal neoplasms located in the alimentary tract. Stromal tumours that arise outside the gastrointestinal tract as primary tumour are designated as extra-gastrointestinal stromal tumours (EGIST). The EGIST are located in mesentry, omentum, retroperitoneum and rarely in pancreas. Only 19 cases of pancreatic EGIST (pEGIST) have been reported in the literature. Of these, there were only two cases of pEGIST with documentation of molecular alteration in C-Kit gene. We here report a third case of primary pEGIST with documentation of C-kit mutation.