RacGAP1 is a protein associated with cell proliferation, cell growth regulation, cell transformation and metastasis. The present study was designed to evaluate RacGAP1 expression in gastrointestinal stromal tumors (GISTs) for the first time in the literature and to determine its association with some predictive clinicopathological features, Ki-67 proliferation index, and risk stratification systems of Armed Forces Institute of Pathology (AFIP) and modified National Institutes of Health (NIH). Paraffin-embedded tissues of 100 GISTs were investigated, retrospectively. High (>= 10%) Ki-67 proliferation index, higher mitotic count, high cellularity, small intestinal location, and highrisk groups according to both AFIP and modified NIH criteria were found to be correlated with RacGAP1 positivity in the univariate analysis (all P values <0.05). The association between RacGAP1 expression and higher cellularity was supported by the multivariate analysis (P=0.023). High (>= 10%) Ki-67 proliferation index was correlated with higher nuclear pleomorphism, necrosis, ulceration, small intestinal location, greater tumor size, higher mitotic count, and high risk group according to AFIP and NIH criteria in the univariate analysis (all P values <0.05). The correlation of Ki-67 proliferation index and mitotic count and high risk group according to AFIP criteria was confirmed by the multivariate analysis (all P values <0.05). In conclusion, higher RacGAP1 expression and Ki-67 index might be considered as effective complementation of risk stratification systems and unfavorable clinicopathological features in predicting poor outcome of GISTs. However, the utility of RacGAP1 expression in GISTs should be further validated in larger cohorts of patients with long-term follow-up data.