The reported incidence and mortality of Clostridium difficile-associated disease has increased significantly, which in part is likely to be due to the emergence of a new, highly virulent strain in North America and Europe. This epidemic strain, referred to as BI/NAP1/027, has increased virulence, attributed to overexpression of the two toxin-encoding genes, tcdA and tcdB, which may be due to truncation of the negative regulator (tcdC) by a 1 bp deletion. In a previous study of whole-genome comparisons using microarray analysis of 75 C. difficile isolates, it was noted that the 20,027 strains, which formed a hypervirulent clade, possessed a unique hybridization pattern for the 7 toxin B microarray reporters. This unique pattern was conserved in all of these 027 strains. The pattern was different for the 55 non-027 strains tested. These data, along with the knowledge that 027 strains are toxinotype III (i.e. possess a complete tcdB gene of comparable size to toxin reference strain VPI 10463), suggest that the sequence of the N-terminal binding domain of toxin B must be divergent from C. difficile strain 630 (and the other 55 strains tested). Additionally, these 027 strains had comparable hybridization patterns across the whole microarray, as well as for tcdB. Therefore, it was suggested that they share a similar, novel N-terminal binding domain. The aim of this study was to ascertain the sequence variation in tcdB from eight characterized BI/NAP1/027 strains. The study confirmed significant sequence variation of tcdB from the sequenced strain 630 and slight variation in tcdB among the eight 027 strains. These results suggest that toxin B from 027 strains may have a different binding capacity compared with its less-virulent counterparts and may, in addition to the mutated tcdC regulator, be responsible for the increased virulence of 027 strains.