Objective To investigate the role of endoscopic ultrasonography-guided fine needle aspiration (EUS-FNA) in the pathological diagnosis of gastrointestinal stromal tumor (GIST) and to examine the cytomorphological features of the obtained specimens along with their indicative significance for gene mutation status.

Methods To analyze the relationship among cellular morphology, immunohistochemistry, and genetic test results, we retrospectively enrolled patients with cytologically and histologically confirmed GIST and available molecular genetic testing results who underwent EUS-FNA at Tianjin Medical University Cancer Institute & Hospital between April 2020 and April 2025.

Results Among 39 cases of GIST confirmed by cytology and immunohistochemical staining, those with KIT mutations were predominantly characterized by spindle or short spindle cell morphology on cytological smears, with occasional observation of epithelioid morphology. The cytological smear of only one PDGFRA-mutated case in this study demonstrated short spindle cell morphology. Cytological smears of KIT/PDGFRA wild-type cells showed a mixture of spindle and epithelioid cell morphologies. Among the eight patients who received preoperative neoadjuvant targeted therapy, postoperative pathological evaluation revealed that one patient showed marked pathological response, six exhibited partial pathological response, and one had no pathological response.

Conclusions Despite the limited sample size, our findings indicate that EUS-FNA cytological smears are of certain reference value for diagnosing GIST. Further analysis identified a potential correlation between the cytomorphological features and gene mutation types, suggesting that utilizing EUS-FNA specimens for pathological diagnosis and molecular subtyping may contribute to the development of precision medicine for GIST.