A rapid method for detecting Escherichia coli O157:H7 combining immunomagnetic beads (IMB) and flow cytometry was developed. Labeling antigens separated by IMB with fluorescent antibody enabled the detection of < 10(3) CFU bacteria per ml in pure culture. The optimum concentration of magnetic beads for flow cytometry was lower (ca. 10(5) particles per ml) than that reported for conventional IMB assay (more than 6 x 10(6) to 8 x 10(6) particles per ml). Immunomagnetic separation and flow cytometry (IMFC) were evaluated for detecting E. coli O157:H7 in the presence of a competing microorganism and for detecting antibodies in potassium phosphate buffer. The total assay time from separating antigens with IMB to analyzing with flow cytometry was about 1 h. IMFC detected 10(3) to 10(4) CFU of E. coli O157:H7 per ml in ground beef enrichment broth and could effectively discriminate between E. coli O157:H7 and competing natural flora. The new assay system provides another approach to separation and detection of low populations of pathogens and shows potential for detecting low concentrations of toxins and other soluble antigens directly from food in a short time.