Seventy cerebrospinal fluid Escherichia coli isolates from infants with neonatal bacterial meningitis (NBM), as submitted to the Netherlands Reference Laboratory for Bacterial Meningitis from 1989 through 1997, were assessed for phylogenetic background and extended virulence genotypes, in comparison with the E. coli reference collection, by using molecular methods. Phylogenetic group B2 significantly predominated overall (81%). The 4 major phylogenetic clusters exhibited distinctive virulence genotypes, suggesting diverse evolutionary histories for the individual genes. Many genes not previously studied in NBM, notably diarrhea-associated cdtB (cytolethal distending toxin [46%]) and urinary tract infection-associated ompT (outer membrane protease T [96%]), were as or more prevalent than traditional NBM-associated traits, such as ibeA (invasion of brain endothelium [33%1), sfaS (S fimbriae [59%]), and K1 capsule (81%). These findings provide novel insights into the phylogenetic origins of NBM-associated E. coli and suggest numerous new potential targets for preventive interventions against this dire disease.