The fecal Escherichia coli population structure may influence the occurrence and etiology of extraintestinal infection, but is poorly understood. Accordingly, fecal E. coli from 39 healthy women (30 putative colonies per subject) were characterized for clonal identity, urinary tract infection-associated virulence traits, and phylogenetic background. The 120 unique E. coli clones (mean, three per sample) were distributed by phylogenetic group as follows: A (33%), D (31%), B1 (19%), and B2 (17%). However, 36% of women carried > or =1 clone from group B2, and 87% had clones from groups B2 and/or D. Of the B2 clones, 90% were from pauciclonal fecal samples (< or =4 clones), compared with 47% and 52% of A and B1 clones (P=.001 and P=.007, respectively). Group B2 and D clones more often were dominant within the source sample than group A and B1 clones (60% vs. 41%: P=.05). Dominant clones exhibited higher virulence scores than non-dominant clones (mean 4.4 vs. 3.1: P=.015). In multilevel regression models, pauciclonal sample, B2, and clonal prevalence significantly predicted virulence score. In conclusion, within the intestinal E. coli population, virulence-associated traits, clonal prevalence, and low fecal clonal diversity are related. Virulence-associated traits of group B2/D E. coli may enhance fitness within the gut, thereby increasing strains' likelihood of causing extraintestinal infection.