We evaluated the detection of terminal deoxynucleotidyltransferase by flow cytometry using two commonly reported methods of permeabilization and compared them with immunofluorescence microscopy. Thirty-four consecutive cases referred for leukemia workup were studied prospectively. We found decreased viability of cells with both flow cytometry methods in association with shifts in forward and side scatter patterns. Both procedures demanded careful manipulation of cells to avoid total lysis. The Triton X-100 method had a sensitivity of 100% and a specificity of 93%, while the methanol method had a sensitivity of 54% and a specificity of 100%. Therefore, the Triton X-100 method correlated better with immunofluorescence microscopy than did the methanol method. Despite technical difficulties, the advantages of increased objectivity, increased diagnostic capability associated with multicolor analysis, and the increased sensitivity in detecting minimal residual disease make flow cytometry a more attractive and advantageous procedure.