Escherichia coli isolates from human blood (n = 266) and faecal (n = 237) samples were examined for cytotoxic necrotizing factors 1 and 2 (CNF 1 and 2), cytolethal distending toxin (CDT), and putative virulence factors that have been associated with disease conditions in humans and animals. PCR showed that the chromosomally encoded, Rho-activating, CNF1 (68/544, 12·5%) was more common than the transmissible plasmid-borne CNF2 (3/544, 0·6%). The relative risk of having either CNF or CDT toxin genes in blood compared to faecal isolates was 3.88 (95% CI 2.36–6.38). This was highly significant (P<0·0001) and demonstrates the importance of these factors in bloodstream infections. Fifty-one of 65 (78%) E. coli bearing CNF1 and 11 of 21 (52%) of E. coli bearing CDT also carried the pyelonephritis-associated pilus gene, papG. The S fimbrial adhesin gene, sfa, was found in 57 blood (21%) and eight faecal samples (3%). The F17 fimbrial adhesin gene and afimbrial adhesin gene afa did not occur frequently. Haemolysin (hly) was found in all of the isolates tested. Further studies must be designed to identify the clinical significance of these genes and their role in pathogenesis.