The complete genomic sequence of a previously characterized temperate phage of Clostridium difficile, phi C2, is reported. The genome is 56 538 bp and organized into 84 putative ORFs in six functional modules. The head and tail structural proteins showed similarities to that of C. difficile phage phi CD1119 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 phi C2 to phi CD119 and the CD630 prophage sequences showed relatedness between phi C2 and the prophages, but less so to phi CD119. phi C2 integrated into a gene encoding a putative transcriptional regulator of the gntR family. phi C2, phi CD119 and CD630 prophage 1 genomes had a Cdu1-attP-integrase arrangement, suggesting that the pathogenicity locus (PaLoc) of C. difficile, flanked by cdu1, has phage origins. The attP sequences of phi C2, phi CD119 and CD630 prophages were dissimilar. phi C2-related sequences were found in 84 % of 37 clinical C. difficile isolates and typed reference strains.