Cytolysins (Cly) I, II, and III are toxins secreted by Actinobacillus pleuropneumoniae. These toxins are thought to play an important role in the pathogenesis of porcine pleuropneumonia. ClyI and ClyII are RTX toxins and in general these toxins are encoded by operons consisting of four genes, C, A, B, and D. Our group recently cloned the C and A genes of the ClyII operon (clyIICA) of serotype 9. We found that this ClyII operon is truncated and lacked intact B and D genes (clyIIBD). B and D genes of the ClyI operon (clyIBD) were present however in serotype 9. In this study we analyzed the ClyII operons of the reference strains of the 12 A. pleuropneumoniae serotypes and compared them with the ClyII operon of serotype 9. We focused on (i) the presence, (ii) the sequence similarity, and (iii) the genomic environment of the clyIICA genes. The presence of the clyIICA sequences was studied by hybridization analysis of genomic DNA. The sequence similarity was studied by restriction fragment analysis on polymerase chain reaction-amplified DNA. The genomic environment was compared by analysis of the sequences that are located 3' of the clyIICA genes. We demonstrated that the clyIICA genes (i) are present in the reference strains of all serotypes, except serotype 10, (ii) have a high degree of sequence similarity, and (iii) are not contiguous with intact clyIIBD genes. We conclude that the organization and nucleotide sequence of the ClyII operons of A. pleuropneumoniae are very similar. We also studied the presence of clyIBD sequences and found them to be present in the reference strains of all serotypes, except serotypes 3 and 6. Thus, in most serotypes the clyIBD genes may complement the absent clyIIBD genes.