An easy and rapid ELISA system, Filtration ELISA, to detect antibodies against bacterial cell surface antigens was developed using a 96-well filtration plate fitted with a 0.22 μm membrane (MultiScreen^®-GV, Millipore). Bacterial whole cells were used as antigens without fixing the cells with formalin etc. The whole cell antigens were washed by vacuum filtration through a filter and resuspended in washing buffer. Assay reactions could be done in the wells without losing the solution. The technique was established using antisera of mice immunized with Escherichia coli, and then evaluated by assaying antibodies to Shiga-toxin producing E. coli O157:H7 (STEC), Staphylococcus aureus and Lactobacillus acidophilus in fecal extracts of 157 children who had eaten school lunches contaminated with STEC in comparison with 25 age-matched control children. The lunch group showed significantly higher IgA antibody titers against STEC than the control group (p<0.0005), but not against L. acidphilus. The results indicate that Filtration ELISA is a quantitative and specific technique for measuring antibodies against antigens on the surface of bacteria without extracting antigens from the bacteria. This technique is widely applicable to the assay of antibodies in various samples including serum and fecal extract against various kinds of bacteria.