To determine the prognostic value of proliferating cell nuclear antigen (PCNA) immunoreactivity in gastrointestinal stromal tumors (GISTs), we analyzed 42 GISTs using the PC10 antibody. Thirty-nine GISTs with adequate follow-up were classified as non-aggressive or aggressive based exclusively on clinical behavior; a 2-year minimum follow-up was required for nonaggressive lesions. The percentage of PCNA-positive nuclei (%PCNA(+)) was significantly greater in colorectal GISTs compared with gastric tumors. No significant differences in %PCNA(+) were observed between gastric and small intestinal or small intestinal and colorectal tumors. The %PCNA(+) strongly correlated with mitotic rate, nuclear pleomorphism, and clinical behavior, whereas size and cellularity weakly correlated with %PCNA(+). Thirty-six GISTs could be classified as having low or high risk for aggressive clinical behavior based on a combination of tumor size, mitotic rate, and %PCNA(+). Twelve of 13 low-risk tumors were clinically nonaggressive, whereas 19 of 23 high-risk tumors were clinically aggressive. This correlation with clinical outcome was highly significant (P = 0.00002). Risk analysis by individual anatomical site also strongly correlated with clinical behavior for gastric (P = 0.0023) and small intestinal (P = 0.0056) tumors. There were too few colorectal GISTs with adequate follow-up and PCNA data for site-specific risk analysis. We conclude that tumor size, mitotic rate, and %PCNA(+) can be used as parameters to predict the clinical behavior of GISTs.