Escherichia coli is a major cause of urinary tract infections (UTI) where the initial infection arises from bacteria originating in the bowel. However, significant differences are observed between the genomes of intestinal and urinary E. coli strains with the latter possessing many adaptations that promote growth in the urinary tract. To define further the adaptation of urinary E. coli isolates the cellular proteomes of 41 E. coli strains, collected from cases of UTI or random faecal samples, were compared by 2-Dimensional Gel Electrophoresis and Principal Component Analysis. The data indicated that individual patients carried relatively homogenous E. coli populations, as defined by their cellular proteomes, but the populations were distinct between patients. For one patient, E. coli, isolated during two recurrent infections 3 months apart, were indistinguishable indicating that for this patient the infections were possibly caused by the same bacterial population. To understand the basis of the discrimination of the bacteria selected protein spots were identified by peptide fragment fingerprinting. The identified proteins were involved in a variety of metabolic and structural roles. The data obtained for these E. coli strains provides a basis from which to target key bacterial proteins for further investigation into E. coli pathogenesis.