BackgroundMesenchymal tumors (MTs) of upper gastrointestinal tract (UGIT) can show morphologic overlap thus posing a diagnostic challenge. This study evaluated the role of endoscopic ultrasound‐guided fine needle aspiration (EUS‐FNA) cytology in the diagnosis of UGIT‐MTs and impact of rapid onsite evaluation (ROSE).MethodsWe retrospectively search our electronic database between January 2001 and August 2019 for cases that underwent EUS‐FNA for a submucosal/or intramural upper GI tract mass forming lesions. Data pertinent to immunostain expression in UGIT‐MTs was also collected.ResultsWe identified 139 cases, of which 72 cases had subsequent surgical resection. The cytologic diagnoses included nondiagnostic, negative, atypical, suspicious for neoplasm and positive for neoplasm (PFN) in 11, 7, 11, 10, and 100 cases, respectively. Diagnosis of PFN was rendered in 51 of 69 cases with ROSE (74%) and in 49 of 70 cases without ROSE (70%). However, the cases with ROSE had a higher percentage of cases being precisely classified than without ROSE (86% vs 61%, P < .05). On comparison of cytologic cases with cell block (CB) (n = 118) and without CB (n = 21), ROSE was performed in 67 (57%) and 2 (10%) cases, respectively (P < .01). All the cases with diagnosis of PFN were confirmed on subsequent surgical resection.ConclusionEUS‐FNA has a diagnostic yield of 72% for UGIT‐MTs. ROSE could improve diagnostic performance by further classifying MTs, probably via securing adequate lesional material for cell block for additional ancillary testing and precise diagnosis.