A whole-cell extraction procedure involving blending soil samples in sodium cholate buffer yielded a bacterial cell suspension suitable for flow cytometric analysis. The method was tested using added bacterial populations detected by immunofluorescence, nucleic acid staining and membrane potential analysis. Selected fluorescent dyes were then used for viability analysis of indigenous bacteria from soil. Numbers determined using fluorogenic ester dyes were greater than those determined from plate counts and equivalent to the number of INT-reducing cells. However, the direct viable count using cell elongation in the presence of cell division inhibitors was the most effective method for direct viability assessment. A further cell purification procedure was also investigated, using lectin-mediated magnetic bead extraction. This resulted in an extremely clean suspension containing uncultured, viable bacterial cells.