Background.Bacteriophages play an important part in gene transfer and gene expression in S.aureus strains and thus also in their virulence and antibiotic resistance.A set of primers for multiplex PCR was designed for identification of prophages of serogroups A,B,F and L in lysogenic and polylysogenic S.aureus strains. Methods.In the genomes of International Typing Set bacteriophages,the sequences specific for both the phage species and serogroups A (ö 3A),B (ö 53),F (ö 77)and L (ö 187)were estimated.The designed primers amplify specific genomic sequences of sizes characteristic of each of the phage species. The multiplex PCR specificity was verified on DNAs of 26 bacteriophages,9 lysogenized and 2 prophageless S.aureus strains. Results.One to three prophages of different serogroups were identified unambiguously in each of 40 clinical strains including 25 MRSA strains.Detectability of prophages by multiplex PCR is comparable with that by phage-specific probes prepared in our laboratory (Doskar et al.,2000,Can.J.Microbiol.46:1066-1076). Conclusions.In view of significant differences in the prophage content between S.aureus closely related isolates,prophage profiling is recommended as a highly sensitive method for strain discrimination.