Type 1 fimbria, an adhesive hair-like structure expressed on the surface of Escherichia coli, functions as a virulence factor in bacterial infections of the urinary tract. The expression of type 1 fimbriae is phase variable and is mediated by an invertible element that can exist in two orientations; the ON orientation allows for fimbriae expression and the OFF orientation blocks fimbriae expression. Although type 1 fimbriae have been shown to contribute to virulence in urinary tract infections (UTI), the specific time during the course of an infection that the fimbriae are expressed has not been demonstrated. To answer this question, a novel quantitative PCR-based assay was used to measure the orientation of the invertible element in a bacterial population infecting the urinary tract. E. coli strains isolated from patients with cystitis and pyelonephritis were cultured under two different growth conditions that favored the position of the invertible element being in one orientation or the other. The pyelonephritis isolates were relatively resistant to switching of the invertible element from the OFF into the ON orientation when compared with the switching patterns of the invertible element of cystitis isolates. In urine samples recovered from experimental UTIs, pyelonephritis and cystitis strains also differed in the control of type 1 fimbriae expression during the course of infection. E. coli strains of cystitis origin switched a greater percentage of their invertible elements into the ON orientation early in infection and maintained the elements in the ON orientation during the entire course of the infections. In contrast pyelonephritis isolates switched a smaller percent of their invertible elements into the ON orientation and failed to maintain this orientation for the entire course of infection. Lastly, it was shown using "locked" mutants of E. coli , that during early infection loss of the ability to express type 1 fimbriae attenuated virulence, while constitutive ability to express the fimbriae enhanced virulence in comparison to the wild type strain. Collectively, this work suggests that expression of type 1 fimbriae is critical during the early stages of urinary tract infections.