Bacterial persistence describes a heterogenous response to antibiotics in clonal populations of bacteria due to phenotypic variation within the population, with a small proportion of cells surviving treatment even at very high concentrations of drug. The aim of this study was to determine whether different natural isolates of E. coli, selected at random from a collection representing the spectrum of genetic diversity in the species, generate different fractions of persister cells. Despite comparable minimum inhibitory concentrations (MICs) to the antibiotics between the different strains, highly significant variation was observed in persister fractions following exposure to ampicillin, streptomycin or norfloxacin. Survival following treatment with one drug did not, however, correlate with survival against another. Finally, using competition assays we quantify fitness benefits of persistence. These results show that different strains of E. coli vary markedly in their response to antibiotics despite comparable genetic susceptibility and indicate different mechanisms of evolved persistence to different antibiotics.