A case of malignant gastrointestinal stromal tumor (GIST) is reported. Histologically, spindle cell proliferation with remarkable whorl formations was predominant in the tumor. Immunohistochemically, the tumor cells were diffusely positive for CD117 (c-Kit) and vimentin and partially positive for CD34. Ultrastructurally, the desmosome-like structures and interdigitations occurred much more frequently in the areas with whorl formations. These organelles were considered to be closely associated with the whorl formations. Various kinds of cellular arrangements are revealed in GISTs, but remarkable whorl formations, such as in our case, are a rare variant pattern. Herein, we discuss the histopathologic differences between this and other tumors showing whorl formations and describe the meaning of this unique arrangement. GISTs are thought to be immature tumors, and, therefore, variations in histopathologic findings are recognized. Finally, the ultrastructural study of GISTs is useful for understanding the mechanisms forming whorl formations and the differentiation or pathogenesis of GISTs.