The use of endoscopic ultrasound-guided fine needle aspiration is expanding rapidly in many centers. This method can be used to produce aspirate specimens from masses in the pancreas, liver, retroperitoneum, adrenals, and mediastinum, as well as mural nodules in the upper gastrointestinal tract. As application of this method continues to grow, it is reasonable to expect that the demand for cytologic diagnosis of gastrointestinal stromal tumors will increase. In this commentary, the cytologic presentation of one such case is offered. This is used to illustrate the clinical, immunohistochemical, and molecular biologic features that are used to suggest the prognosis of a given lesion.