Clostridium perfringens causes many human and animal diseases and can secrete up to 16 different extracellular toxins and enzymes. The genes encoding many of these toxins are located on large, potentially conjugative, plasmids. Many strains contain more than one toxin plasmid and several of these plasmids have been shown to have up to 35 kb of sequence homology, including regions involved in replication, plasmid maintenance and conjugation. All of these sequenced plasmids have an almost identical rep gene, confirming that they are members of a related plasmid family. The plasmid maintenance region comprises genes related to the parMRC family and four incompatibility groups, parMA to D, have been identified. We have compared the sequences of several toxin plasmids from a C. perfringens type C isolate and a type D isolate of animal origin. These plasmids carry the cpb and tpeL toxin genes (type C) and the etx, cpb2 and cpe toxin genes (type D), all of which are plasmid encoded. We showed that the type D strain contained four large plasmids, two of which were conjugative and were related to previously sequenced toxin plasmids, but had differences in their respective plasmid maintenance regions. One plasmid encoded a novel replication protein and the second plasmid encoded a putative parM gene with limited homology to the existing parM homologues; it therefore belongs to a new plasmid incompatibility group. In addition, although the type C plasmid was conjugative, marked plasmid instability was observed; subsequent sequence analysis suggested that this plasmid consisted of a fusion between two separate plasmids. In conclusion, these studies have indicated that there is an even greater diversity between C.perfringens toxin plasmids than was previously thought. It is clear that there still is much more to learn about the toxin plasmids of C. perfringens.