DNA ploidy was investigated by flow cytometry (FC) and image analysis (IA) in paraffin-embedded tissue sections from 36 stromal tumors of the gastrointestinal tract. The results of both techniques were correlated with pathologic features of the tumors and survival. Ten (27.8%) tumors were aneuploid by FC and IA. Most of the diploid tumors were identified by both techniques, but FC appeared to be superior to tissue section IA for identification of aneuploid tumors (25% vs. 13.8%). Aneuploidy by FC correlated with pathologic grade and mitotic index (P < .05), and a trend to short survival was also detected (P < .1). No similar correlation was found by IA. Enlargement and variation of nuclei may explain the discrepancy between FC and IA.