Uropathogenic Escherichia coli (UPEC) cause the majority of community-acquired urinary tract infections (UTIs). Quantitation of bacteriuria (the number of bacteria in urine) is important for diagnostic approaches and in diverse research applications. Most UPEC strains express hemolysin, the expression of which has been correlated with the severity of UTI in murine models of infection. In this study, we sought to develop and optimise a quantitative Polymerase Chain Reaction (qPCR) assay for enumeration of hemolysin-positive UPEC in urine. Using recombinant plasmid pJET1.2::hlyD, which we termed pGU2470, the sensitivity range and linearity of amplification of qPCR was determined using primers and a probe targeting hlyD. Whole-cell preparations containing UPEC were quantified for hlyD copy number using CT values and compared to standards prepared with a known amount of pGU2470. We compared the efficiency of the assay for analysis of human and mouse urine because mouse models of human UTI are frequently used for investigating UPEC UTI. Urine samples were collected from healthy adults and mouse infection assays and used to assess any potential inhibitory effects of urine on the qPCR. The linear quantitative range of the qPCR (i.e. sensitivity) in detecting UPEC genomes was 103 copies/ml; qPCR-derived estimates of UPEC bacteriuria (based on number of genomes detected) were, on average, ten-fold higher that culture-based estimates. Finally, the frequencies of positive and negative predictions of UPEC in urine using the qPCR were equivalent to colony count methods. This assay provides an alternative to culture-based approaches for quantitation of UPEC bacteriuria in research studies.