The subtype of verotoxin 2 (VT2) found in 22 VT2-positive stool samples from severely diseased Italian and German children with haemorrhagic colitis or haemolytic uraemic syndrome, or both, and that produced by the corresponding VT-producing Escherichia coli (VTEC) strains isolated from the stools were studied by cytotoxicity seroneutralisation assays and by polymerase chain reaction (PCR) amplification of the VT2 B-subunit gene, followed by restriction fragment length polymorphism (RFLP) analysis. The free faecal toxin was serotyped as the classical VT2 in 21 stool samples, and as the VT2 variant VT2c in one. For all but one of the VTEC isolates, the toxin phenotype was consistent with the type of VT produced in vivo and found in the corresponding stool samples. Genotyping was in agreement with phenotyping for those strains harbouring a single type of VT2 gene. Three O157:H7 isolates carrying both VT2 and VT2c genes had the VT2 phenotype, instead of the expected VT2c phenotype. Direct PCR analysis of stools detected VT genes in only 11 of 20 VT-positive stool samples suggesting that the Vero cell cytotoxicity assay is more sensitive in diagnosing VTEC infection. Immunological and genetic subtyping of VT2 performed directly on stool samples from patients with haemolytic uraemic syndrome could be a useful complementary approach to understanding the role of the different types of VT in this syndrome.