In an attempt to compare results of fresh and fixed tissue flow cytometric DNA analysis we analyzed paraffin blocks of 87 solid tumors; 67 of these were DNA aneuploid and 20 were DNA euploid by fresh flow cytometric analysis. Forty-two aneuploid tumors and all diploid tumors were concordant (71.3% concordance), whereas 25 of 67 (37%) aneuploid tumors appeared diploid on fixed tissue analysis. Reasons for discordance included loss of small aneuploid peaks, merging of G1/G0 peaks of diploid and aneuploid stemlines giving a broad G1/G0 peak, and masking of near-tetraploid aneuploid peaks by the G2/M peak in fixed tissue. S-phase fraction could be determined in 51 of 67 (76%) aneuploid cases analyzed fresh and 29 of 42 (69%) concordant aneuploid cases analyzed from fixed tissues. All parameters were consistently higher in the fixed tissue: S-phase fraction (mean = 18.29% versus 12.82%), coefficient of variation of diploid G1/G0 peak (5.62% versus 2.11%), and DNA index (1.79 versus 1.69). We conclude that significant differences exist between flow cytometric data obtained from analysis of fresh versus fixed tissues and therefore prognostic correlations made on the basis of results of fixed tissue flow cytometric analysis may not necessarily parallel those of fresh tissue studies.