Background: Recently developed adjuvant therapies for gastrointestinal stromal tumor (GIST) have been shown to improve patient survival. Guidelines currently recommend contrast-enhanced computed tomography (CECT) for GIST detection and surveillance. Patients with moderate-to-high risk GISTs require more frequent surveillance due to a higher 5-year recurrence rate. Our study aimed to compare noncontrast magnetic resonance imaging (MRI) with CECT for GIST detection, and evaluate volumetric apparent diffusion coefficients (ADCs) for risk stratification of GIST. Methods: We retrospectively enrolled 83 patients with histopathologically confirmed GISTs for lesion detection efficiency analysis between noncontrast MRI and matched CECT studies. A 5-point scale was used by two independent reviewers to determine if the lesion was present or absent. Another cohort, comprising 28 patients with pathologically confirmed primary GISTs, was further screened for risk stratification, with a comparison of volumetric ADC parameters between the pathologically very-low-to-low risk and moderate to-high risk GIST patients. Results: For identifying GISTs, the sensitivity and specificity of noncontrast MRI were 83.6% and 89.3% for reader 1 respectively, and 81.8% and 92.9% for reader 2 respectively; the sensitivity and specificity of CECT were 76.4% and 89.3% for reader 1 respectively, and 76.4 and 78.6% for reader 2 respectively. Tumor volumetric ADC histogram parameters, including ADCmax, ADCstdev, 90th and 95th percentiles, inhomogeneity, and entropy, were positively correlated with a higher risk grade of GIST (r=0.421-0.758). The receiver operator characteristic curve analysis showed ADCmax achieved the highest area under the curve value of 0.938 for discriminating very-low-to-low risk versus moderate-to-high risk GISTs. Conclusions: Noncontrast MRI was an efficient technique for identifying GIST patients. The combination of CECT and noncontrast MRI can improve the reliability of diagnosis. For patients with contraindications to CECT, noncontrast MRI may be a comparable alternative. Volumetric ADC histogram parameters may be useful in differentiating very-low-to-low risk from moderate-to-high risk primary GISTs.