Comparisons between flow cytometry (FCM) and image cytometry (ICM) have found a high concordance rate in pancreatic tissue, with some discrepancies between the two procedures. This study utilized 40 cases of chronic pancreatitis, primary pancreatic adenocarcinoma and metastatic pancreatic adenocarcinoma to determine the concordance rate between the two procedures. The reasons for discrepancies were identified and subsequently used to establish methods for a priori determination of which procedure to use. Using the FACSCAN flow cytometer and the CAS 200 on appropriately stained specimens that were disaggregated from 50-micron sections, we achieved a concordance rate of r = .878 (P < .01) after removing outliers. Thirty-one of 40 cases matched DNA content, and 9 cases had discrepant results. These discrepant cases were evaluated with factor analysis, in part because initial observations suggested that the variables evaluated could be combined into unifying concepts. The nine measured variables were compressed into three factors, which accounted for 68% of the variation observed between the two methods. Readily evaluated features, on a case-by-case basis, including tumor/nontumor ratios, accounted for the largest proportion of this variation. These findings suggest that tumor/nontumor cell ratios in hematoxylin-eosin-stained sections may provide adequate a priori information to direct the choice of either FCM or ICM to measure DNA ploidy in pancreatic tissue.