Flow-cytometrically measured DNA content of 58 surgically resected gastrointestinal stromal tumors (GIST) was correlated with the lesions' histopathologic features and patients' survival. Aneuploid DNA patterns were found in 43 cases (74%), including 33 (76.7%) histologically malignant and 10 (23.3%) in the indeterminate category. DNA ploidy pattern was significantly correlated with mitotic count (less than 5/10 high power field (HPF) versus greater than or equal to 5/10 HPF, P = 0.04) and histologic grade (malignant versus indeterminate, P = 0.02). DNA content was not related to tumor size, site, or histologic patterns (epitheliod versus spindle). The patients' survival was significantly correlated with DNA content (P less than 0.001), histologic grade (indeterminate versus malignant, P = 0.02), and mitotic rate (less than 5/10 HPF versus greater than or equal to 5/10 HPF, P = 0.01). Multivariate regression analysis showed that DNA ploidy is an independent parameter in predicting the clinical outcome for patients with GIST.