Erwinia amylovora is the causative agent of fire blight, a very destructive disease of numerous members of the rosaceae. The primary route of infection for host species, including commercially grown apple and pear, is the newly opened blossom. Susceptibility of flowers to infection for only a few days creates narrow window for infection. Not surprisingly, the risk of disease is related to E. amylovora population size. As a result, methods that supply quick, accurate and sensitive quantification of the pathogen population are important tools for determining the need for and the efficacy of disease control intervention. Plating samples and assessing colony-forming units constitutes an accurate and sensitive but slow method. Endpoint PCR is quick and sensitive but is not particularly amenable to quantification. We describe a real-time PCR procedure that provides all requirements. This method is based on chromosomal genes rather than on the pEa29 plasmid and so can be used to measure isolates that have been cured of the plasmid. The method has been used very successfully in directly quantify whole E. amylovora cells, in a variety of tissues from the orchard environment.