We describe an improved multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) scheme for genotyping Staphylococcus aureus. We compare its performance to those of multilocus sequence typing (MLST) and spa typing in a survey of 309 strains. This collection includes 87 epidemic methicillin-resistant S. Staphylococcus aureus is a pathogen of worldwide clinical significance. For this reason, it is the subject of intensive investigations in terms of virulence and drug resistance phenotypes and, also, population genetics. Although the latter is not of significant use for short-term patient care, it is essential for understanding the emergence and spread of new phenotypes. For instance, it was initially considered most likely that methicillin (meticillin)-resistant variants were appearing only rarely through the acquisition of a mobile DNA region designated staphylococcal cassette chromosome mec (SCCmec) and that these variants were spreading efficiently worldwide (34). However, the most recent population genetics investigations suggested instead that SCCmec was acquired hundreds of times independently worldwide and that, as a rule, the geographic spread of these resistant strains was limited (28,36). This knowledge could be produced in the past 10 years due to sequence-based approaches, mainly multilocus sequence typing (MLST) analysis, in which approximately 3 kb of coding genome sequence (or 1/1,000 of the whole genome) are scanned for polymorphism. MLST has allowed the creation of shared and high-quality databases which can be easily queried over the Internet, and this has proved to be highly valuable (7). However, as the sequences used in MLST schemes evolve slowly and are highly conserved, the resolution provided by MLST is too low for the investigation of recent evolution and, above all, for short-term epidemiological studies. The sequencing of much larger portions of the genome to increase resolution can only be used in dedicated research projects analyzing a limited number of strains (28). Presently, pulsed-field gel electrophoresis (PFGE) remains the most discriminatory technique for S. aureus typing, but it allows the constitution of shared databases only at the national level and is not appropriate for population studies (1, 35). There is, consequently, still a need for a technology as discriminatory as PFGE and as portable as MLST at a low cost.Tandemly repeated sequences provide a very valuable source of polymorphism. Multilocus variable-number tandemrepeat (VNTR) analysis (MLVA) is now used in genotyping several bacterial species (26,48). MLVA typing relies upon a basic and widespread methodology, the measurement of the length of DNA fragments. It is not a "pattern"-producing method, even when run on agarose gels. The genotype, in the form of a string of numbers corresponding to the number of repeats at each locus, is highly portable and can be readily incorporated in large databases (13).