Infections with bacteria producing shiga toxin are responsible for widespread disease and for the death of a large number of people. In the present study, we have developed a rapid method of high specificity for the detection of Shigella dysenteriae by combining immuno-capture of the bacteria and polymerase chain reaction (PCR) amplification of their toxin gene. We compared the sensitivity of our new method, referred to as immuno-capture toxin gene PCR (iTGPCR), with a conventional TGPCR (cTGPCR) method in detecting S. dysenteriae. Approximately 100 colony forming units (CFU) of bacteria in a volume of 400 µl were divided into 20 tubes with 5 CFU (20 µl). One group of 10 tubes was analyzed by iTGPCR and the other by cTGPCR amplification. All were positive in the 10 tubes using iTGPCR but, in contrast, only half were positive in the 10 tubes with the cTGPCR method. This method was used to detect S. dysenteriae type I in sewage samples without the normal tedious preparation methods. These findings suggest that iTGPCR gives enhanced test sensitivity, and allows determination of pathogen serotype, and differentiation of toxin-producing strains from non toxin-producing strains.