Clostridium perfringens is an important pathogen of humans and animals. Certain strains of type A isolates cause necrotic enteritis (NE) in broiler chickens, a common infection. A major breakthrough in understanding virulence in NE isolates of C. perfringens was the demonstration that a new toxin, NetB, is critical for development of the disease. A netB-positive (pNetB-NE10) and a cpb2-positive plasmid (pCpb2-CP1) obtained from NE isolates were shown to be conjugative, and the plasmids were completely sequenced. Both plasmids possessed the large conjugative region characteristic of C. perfringens conjugative plasmids (CpCPs). Comparative genomic analysis of nine CpCPs, including the two plasmids described here, showed extensive gene rearrangements including pathogenicity locus and accessory gene insertions around rather than within the backbone region. The pattern that emerges from this analysis is that the major toxin-containing regions of the variety of virulence-associated CpCPs are organized as complex pathogenicity loci.