Streptococcus suis (S. suis) is an important pathogen that can carry prophages. Here we present a comparative genomic analysis of twelve (pro)phages identified in the genomes of S. suis isolates. According to the putative functions of the open reading frames predicted, all genomes could be organized into five major functionally gene clusters involved in lysogeny, replication, packaging, morphogenesis and lysis. Phylogenetic analyses of the prophage sequences revealed that the prophages could be divided into five main groups. Whereas the genome content of the prophages in groups 1, 2 and 3 showed quite some similarity, the genome structures of prophages in groups 4 and 5 were quite distinct. Interestingly, several genes homologous to known virulence factors, including virulence associated protein E, a toxin-antitoxin system and a DNA methyltransferase were found to be associated with various (pro)phages. This clearly indicates that these (pro)phages can contribute to the virulence of their hosts.