The complete genomic sequence of a previously characterized temperate phage of Clostridium difficile, φC2, is reported. The genome is 56 538 by and organized into 84 putative ORFs in six functional modules. The head and tail structural proteins showed similarities to that of C. difficile phage φCD119 and Streptococcus pneumoniae phage EJ-1, respectively. Homologues of structural and replication proteins were found in prophages 1 and 2 of the sequenced C. difficile CD630 genome. A putative holin appears unique to the C. difficile phages and was functional when expressed in Escherichia coli. Nucleotide sequence comparisons of φC2 to φCD119 and the CD630 prophage sequences showed relatedness between φC2 and the prophages, but less so to φCD119. φC2 integrated into a gene encoding a putative transcriptional regulator of the gntR family. φC2, φCD119 and CD630 prophage 1 genomes had a Cdu1 -attP-integrase arrangement, suggesting that the pathogenicity locus (PaLoc) of C. difficile, flanked by cdul, has phage origins. The attP sequences of φC2, φCD119 and CD630 prophages were dissimilar. φC2-related sequences were found in 84 % of 37 clinical C. difficile isolates and typed reference strains.