Background and purpose: Gastrointestinal stromal tumors (GISTs) are rare diseases of the gastrointestinal tract but they are the most common gastrointestinal tumors of mesenchymal origin. Since most GISTs have malignant potential, their probability of malignant progression must be evaluated. This study was conducted to examine the correlation between three-dimensional GIST volume measured by CT and malignant potential. Materials and methods: A retrospective study was performed on 70 patients diagnosed with GIST after surgical resection in Hanyang University Seoul Hospital from 2012 to 2017. Linear regression analysis was used to establish which between the length of the long axis of GISTs, originally considered a predictor of malignancy, and their volume was a more accurate predictor of malignancy. Tumor dimensions were measured by CT. Results: Data were analyzed using the chi-square test or Student’s t-test and logistic regression. Of the GISTs, 53 (75.71%) were in the stomach, 3 (4.29%) in the small intestine, and 14 (20.0%) in the large intestine. The mean age of the malignant GIST group was significantly higher than that of the benign GIST group (p = 0.032), their tumor long axes were significantly greater (p = 0.073), their tumor volumes were significantly larger (p = 0.001), and the frequency of tumor necrosis was higher (p = 0.001). In multivariate analysis, malignant GIST was associated with location in organs other than the stomach (OR 7.846, 95% CI 1.293–47.624, p = 0.025), longer axis (OR 1.037, 95% CI 1.011–1.065, p = 0.006), larger volume (OR 1.003, 95% CI 1.000–1.006, p = 0.029), and necrosis (OR 12.222, 95% CI 1.945–76.794, p = 0.008). The mean age of the recurrent GIST group was higher than that of the non-recurrent group (p = 0.045), their tumor long axes were significantly longer (p = 0.005), and their volumes were greater, but this last difference was not significant (p = 0.072). Conclusions: Tumor volume can be considered an additional risk factor in assessing the malignant potential of GISTs and tends to increase in recurrent GISTs.