The present study reports the diagnostic utility of endoscopic ultrasound-guided fine needle aspiration (EUS-FNAC) in two patients affected by gastrointestinal stromal tumours (GISTs) of the stomach. Clinically, the patients demonstrated skin pallor, melena, gastric discomfort and pain that had lasted three days or weeks. The cytological findings are discussed; these were strongly supported by immunocytochemical procedures that were performed on cell blocks and further confirmed following post-surgical histopathological examination. The crucial aim of GIST management is to determine a correct diagnosis in early-phase disease in order to realize an adequate curative surgical resection before the tumour becomes unresectable or metastatic. Moreover, a correct pre-surgical differential diagnosis of GISTs from other mesenchymal neoplasms may be easily made by EUS-FNAC, supported by cytological and immunocytochemical features.