Objective: The aim of this study was to investigate the value of multi-slice spiral CT (MSCT) in the diagnosis of malignant gastrointestinal stromal tumors (GISTs). Methods: Twenty-seven cases of MSCT images of malignant GIST proved by surgery and pathology were retrospectively analyzed. Both plain and enhanced CT scan was performed and multiplanar reconstruction was made in all cases. Results: The lesions originated from the stomach (n = 11), small intestine (n = 9), colon (n = 4), rectum (n = 1), and mesentary (n = 2). The transverse diameters of mass were 4.2-22 cm, the edges clearly (n = 12),unclearly (n = 15). The mass were mainly irregular in shape lobulated (n = 19). The lesions were mainly heterogeneity on plain scan, moderate to marked enhancement in arterial phase and durative enhanced in venous phase. Cystic necrosis were observed in all the lesions, 9 cases were cystic and solid mixed mass. Hepatic metastases (n = 4), pulmonary metastasis (n =1), lymphatic metastasis (n = 2) were detected. The accuracy rate of MSCT diagnosis for location and pathologic features of GISTs were 85.2% (23/27) and 77.8% (21/27). Conclusion: Two-phase MSCT examination and axial images combined with multiplanar reconstruction images have important value for diagnosis of malignant GIST.