A rapid method combining flow cytometry and immunomagnetic bead separation (IMFC) was effective for detecting low populations of Escherichia coli O157:H7 inoculated into ground beef, apple juice, and raw milk samples. Modified buffered peptone was most effective for enrichment of E. coli O157:H7 in ground beef. Using IMFC in combination with a 6-h enrichment, as few as four E. coli O157:H7 cells/g of ground beef were detected in as little as a 7-h total analysis time. Our results demonstrate the possibility of using flow cytometry and immunomagnetic bead separation to detect low concentrations of E. coli O157:H7 in ground beef, apple juice and milk.