Flow cytometric analysis of intratumoral DNA stemline heterogeneity was carried out in 48 patients who underwent liver resection for hepatocellular carcinoma (HCC). The nuclear DNA content was determined in specimens cut into one centimeter square pieces; all specimens had been taken from the largest section of the tumor. Of the 48 tumors twelve (25%) were diploid (group D), 11 (22.9%) had both diploid and aneuploid patterns (group DA), and the remaining 25 (52.1%) were aneuploid (group A). Out of 25 group A tumors, eleven had two or more different aneuploid peaks (multiple aneuploid). Thus, DNA stemline heterogeneity was present in 22 tumors (45.7%). With respect to survival, patients with group A tumors had a significantly poorer prognosis than did those with group D tumors, irrespective of tumor size. In group DA patients, the outcome was influenced by the "poor" prognostic nature of the positive DNA aneuploidy. Thus, HCC has a higher incidence of intratumoral DNA heterogeneity than previously considered, and the prognosis for patients with a positive aneuploidy pattern is poor.