A major problem with flow cytometric analysis of clinical solid tumor specimens is that of non-malignant cell contamination which contributes to inaccurate results. Monoclonal antibody to cytokeratin, a marker for epithelial tumor (carcinoma) cells, was successfully used in conjunction with a DNA-specific dye to dually stain specimens so as to obtain DNA profiles exclusively for marker-positive tumor cells. This gating procedure was used also for analysis of the cell marker distribution for those cells having a DNA content consistent with aneuploidy. After successful verification in model systems, clinical carcinoma specimens were studied. The aneuploid population increased from a mean of 61% without gating to a mean of 81% with gating for cytokeratin. The cytokeratin-positive cell fraction increased from a mean of 55% without gating to a mean of 96% with gating for aneuploid DNA content. This gating procedure makes it possible to associate cell markers confidently with tumor cell populations, thus providing objective verification of the tissue of origin for these tumors. It can be performed simultaneously with standard gating for DNA analysis; and both procedures used together, cross-gating, are invaluable for more precise analysis of human tumor DNA and cell markers.