The DNA content of neoplasms is generally determined by flow cytometry, but quantitative microscopic image analysis is an alternative technique for DNA quantification. To compare these two methods, the DNA content of 31 paraffin-embedded canine transitional cell carcinomas was measured by flow cytometry and image analysis. Interpretable data were available for 26 samples by flow cytometry and 27 samples by image analysis. For 23 neoplasms with interpretable data by both methods, a good correlation (r = .80, P < .001) was obtained between the DNA indices determined by flow cytometry and image analysis. Concordance of DNA ploidy classification was reached in 21 samples; however, for 4 samples an aneuploid cell population, usually tetraploid, was identified by image analysis and not by flow cytometry. Two samples also had aneuploid peaks by flow cytometry and not by image analysis. Although a good correlation was seen between the measurement of DNA content Of paraffin-embedded canine tissue by image analysis and flow cytometry, this study did demonstrate that aneuploid cell populations can be missed by both methods and that image analysis was better than flow cytometry in the detection of aneuploid cell populations, particularly tetraploid ones, in samples with excessive cellular debris.