Purpose: In this retrospective study, we investigated the clinicopathologic features, prognosis as well as the factors contributing to prognosis of patients with metastatic or recurrent gastrointestinal stromal tumors (GISTs). Methods: A total 142 GIST patients with confirmed metastasis or recurrence with complete clinicopathologic and prognostic data were enrolled as research group, and 278 GISTs patients without metastasis or recurrence as control group between June 2003 and June 2013. Results: Significant differences between research group and control group were revealed, including gender, age, primary tumor sites, tumor diameter, mitosis rate, CD117 expression, risk level, treatment methods and surgical types (p < 0.05). Univariate survival analysis suggested that factors with significant influence on prognosis were tumor primary site, tumor diameter, mitosis rate, tumor progression (recurrence or metastasis), and treatment methods (p < 0.05). Multivariate survival analysis demonstrated that mitosis and treatment methods were independent prognostic factors for GIST patients with metastatis or recurrence. Conclusion: Some factors contributed significantly to the prognosis of GIST patients with metastatis or recurrence, and the combination of surgery and targeted agent should be selected for these patients to improve prognosis.