BACKGROUND: The preoperative radiological diagnosis of GIST is complicated by its varied macroscopic morphology. Moreover, the precision of preoperative histopathological diagnostics is reduced by the submucosal localization of the lesion. OBJECTIVES: The goal of the study was to perform a retrospective analysis of the clinical and histopathological factors seen in patients operated on for a stomach GIST tumor with unclear diagnosis. MATERIAL AND METHODS: Two groups of GIST patients treated in our department were compared with regard to their histopathological and clinical data. The first group (9 patients, group 1) comprised patients with a histopathological diagnosis for stomach GIST confirmed before the surgical procedure, while the second group (10 patients, group 2) comprised patients with no solid histopathological diagnosis before surgery. The following clinical and histopathological variables were analyzed in the study: age, gender, presence or absence of metastases, anatomical location of metastases, symptoms, tumor size, surgical mortality, tumor recurrence, treatment with imatinib, patient survival in months, histological subtype, mitotic index, cellular atypia, necrosis, tumor ulceration and Ki-67. The results were analyzed statistically. RESULTS: The mean survival time differed significantly between the two study groups: group 1 being 12 months and group 2 being 8 months. The lower survival time in group 2 was connected with the higher stage of the disease at the moment of diagnosis. CONCLUSIONS: Our findings suggest that GIST tumors with an unclear diagnosis are recognized at a late stage of the disease. The more advanced stage of the tumor probably results from faster tumor growth caused by higher proliferation activity. These GIST tumors are characterized by a lower survival rate due to the later stage of the disease at the time of diagnosis.