Gastrointestinal stromal tumors (GIST) may present with myogen or neurogen differentiation, mixed differentiation or with morphological features which cannot be further specified. 14 GIST of the stomach (9), the duodenum (2) and small bowel (3) were examined by immunohistochemistry and electron microscopy. Diagnosis was consistent for such tumors located distally from the stomach, however, evaluation of GIST of the stomach was different (apart from one case). Light microscopy and immunohistochemistry did not allow to discriminate between the different subtypes of GIST, however, electron microscopy revealed cellular differentiation. Hence, ultrastructural analysis is an useful tool for diagnosis of GIST, particularly those of the stomach.