Objective: The aim of this study was to analyze the clinical pathological features of the atypical glomus tumor of the stomach, and explore its biological behavior and clinical significance. Methods: a 43-year-old female was admitted due to passing black stool for 5 months. The melena of the patient occurred after eating the crabs. The endoscopic ultrasonography (EUS) was performed, showing a hypoecho nodule found at the body of the stomach, suggesting the diagnosis of gastric stromal tumor. After onset of disease, no specific clinical symptoms were observed except for the slight feeling discomfort in upper abdominal region. The gastroscopy was performed under the general anesthesia: there was a spheroidal nodule measuring 2.5 cm x 3.0 cm at the anterior wall of the body of stomach near the side of lesser curvature with the focal erosion of gastric mucosa. The DualknifeTM and the snare were used to excise the tumor in full thickness. Grossly, the tumor nodule measured 2.5 cm in diameter. The cut surface was solid, showing moderate consistency and grey red in colour. Microscopically, this tumor presented a well circumscribed nodule. It composed of the rounded neoplastic cells which were mainly arranged in solid pattern. The tumor cells had well-defined cell membranes, centrally placed, round nuclei and amphophilic cytoplasm. Immunohistochemical staining showed the positive expression of smooth muscle actin (SMA), caldesmon and vimentin; meanwhile detecting the negative expression of desmin, pan-cytokeratin, CD34, CD117 and S-100 in tumor cells. The Ki-67 labelling index of tumor was 8%. Results: Combined with the histopathological features, immunophenotype of the tumor, deep location in abdominal cavity and with greater diameter larger than 2 cm, and the diagnosis of atypical glomus tumor of the body of the stomach in this case was established. Conclusion: The atypical glomus tumor of the body of the stomach is a rare mesenchymal tumor. The following differential diagnosis should be included as following: gastrointestinal stromal tumor (GIST), paraganglioma, myopericytoma and the angioleiomyoma. The immunohistochemistry exerts an essential role during the diagnosis of this tumor. The deeper location and larger size implicate its undetermined biological behavior. © Huazhong University of Science and Technology and Springer-Verlag Berlin Heidelberg 2012.