Rectal gastrointestinal stromal tumors (GIST) account for 0.1% of all rectal tumors. They are generally diagnosed in adults over 50 years of age with non-specific symptoms. Immunohistochemistry performed on biopsy tissue sample confirms the diagnosis. In this study, we report two cases of histologically and immunohistochemically confirmed rectal GISTs diagnosed using Endoscopic ultrasound (EUS) with fine needle aspiration (FNA), a procedure of crucial value in the diagnosis of these tumors. Both patients were male, presenting with non-specific symptoms. Standard endoscopy showed a rectal mass in both cases, biopsies were negative. EUS showed a well-defined hypoechoic mass and evaluated adjacent organs and of blood/lymphatic nodes involvement. EUS-FNA was performed in both cases. Cytology and immunocytochemistry studies showed spindle cell pattern with positive immunohistochemical staining for CD117, typical of GISTs.