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The diagnosis of gastrointestinal stromal tumors (GISTs) is generally straightforward using a combination of histologic evaluation and pertinent immunohistochemical staining with CD117/kit and DOG-1 (discovered on GIST) antibodies. However, this tumor can be challenging in cases with an unusual morphology, in limited biopsies, for those in uncommon sites, post-treatment, and when other neoplasms express CD117/kit and DOG-1, thereby mimicking GIST. Finding epithelioid GISTs in the stomach in younger patients should prompt testing for succinate dehydrogenase (SHD)-deficiency using immunohistochemical staining for subunit B (SDHB). However, SDH-deficient GISTs can also arise in older patients, or as part of the Carney triad or Carney-Stratakis syndrome. GISTs with PDGFRA mutations can also prove difficult if they lack kit expression. It is also important to consider morphologic and immunophenotypic changes associated with treatment, including the potential absence of kit expression, particularly in GISTs that have metastasized. Therefore, obtaining clinical information regarding prior therapy with a tyrosine kinase inhibitor (TKI) is crucial.