Gastrointestinal stromal tumor (GIST) is the most common mesenchymal tumor of the gastrointestinal tract (GI). Although positive immunohistochemistry for c-kit protein (CD117) and CD34 is critical in establishing diagnosis, the clinicopathologic features of CD117-positive mesenchymal tumors without obvious connection to the GI tract are not well documented. We describe the clinicopathologic features of two cases of extra-GIST. Case 1 was a 42-year-old woman who presented with a submucosal tumor located in the posterior vaginal wall. Case 2 was a 66-year-old woman who presented with a mass that bulged from the right side of the middle vaginal wall. Both tumors were excised locally. The results of microscopic examination and immunohistochemistry for both cases indicated the diagnosis of GIST. Case 2, in addition, showed oncogenic mutation in KIT exon 11. Case 1 is healthy without evidence of recurrence 4 years after surgery. Case 2 started imatinib therapy after resection of a recurrent mass. Gynecologists as well as diagnostic pathologists should be aware of GIST manifesting as a vaginal mass. Recognition of microscopic patterns and characteristic immunohistochemical phenotype, plus genetic study, is mandatory for establishing the correct diagnosis of GIST.