The closely related Clostridium novyi and Clostridium botulinum types C and D are of current interest because of their association with serious infections in injecting drug users (C. novyi type A) and equine and feline dysautonomias (C. botulinum types C/D). The species are defined by the major toxins they produce: the alpha toxin of C. novyi, and the type C and D neurotoxins of C. botulinum (BoNT/C and BoNT/D). The other major toxin produced by this group, and previously thought to be restricted to the botulinum types, is the chromosomally encoded C2--a binary toxin consisting of two components, I and II. In the current study 44 of these clostridia from the authors' culture collection were investigated--most of which had been identified previously by conventional biochemical tests as 'C. novyi type A'. The aim was to check the distribution of toxin genes by PCR to see if the identities were consistent with the genes carried, and to ascertain if the C2 gene was only found in authentic C. botulinum strains. Several combinations of the species-defining genes and the two components of the C2 genes were detected. Only the authentic BoNT/C- and BoNT/D-positive C. botulinum strains and one of two non-neurotoxic variants of type C carried genes for both components of the C2 toxin. Of the remaining 40 C. novyi type A-like strains, the gene for the alpha toxin was found in 22, with 19 of these also possessing the gene for component I (16) or component II (3) but not both. In the alpha toxin-negative strains (22), both of the C2 genes were detected in 5 strains (3 C. botulinum), with component I in 11 strains and neither gene in 6 strains.