SummaryDNA Ploidy and S phase fraction (SPF) were measured in Stage I and II breast cancers from patients with at least 8 years of follow-up, to assess the prognostic significance of these data. Disaggregated sections of formalin-fixed, paraffin-embedded tumour were analysed by flow cytometry. SPF was calculated using a rectangular model of S phase, after subtraction of background debris using an exponential model. 64% of tumours were DNA aneuploid. The median SPF was 4.5% for DNA diploid, and 10.9% for DNA aneuploid tumours. There were small reductions in survival at 10 years for DNA aneuploid tumours, and for tumours with above median SPF, but these were not statistically significant. The relative hazard for DNA aneuploid tumours was 1.20 (95% CI 0.81-1.76), and for high SPF was 1.31 (95% CI 0.87-1.98). Neither factor was statistically correlated with survival in multivariate analysis. Technical and theoretical factors limit the accuracy and reproducibility of flow cytometric data, and may explain the lack of prognostic information given.Since the publication of a technique for using paraffin embedded tissue for flow cytometry (Hedley et al., 1983) (Hedley et al., 1985). All presumptively DNA aneuploid histograms showed a substantial population of DNA diploid cells, which acts as an internal standard. Histograms were classified as DNA aneuploid if more than one discrete population was identified. The DNA index was then assigned as the ratio between the mean channel number for the aneuploid GO/GI peak, and the mean channel for the GO/GI peak of the normal cell population within the histogCorrespondence: