Over the last decades S.aureus evolved to Methicillin Resistant S.aureus (MRSA) and community acquired MRSA. Most of the molecular characteristics defining the different strains are detectable using nucleic acid based tests. Therefore, genotyping has become more important to differentiate S.aureus. Molecular typing strategies such as spa-, agr-, SCCmec- and multilocus sequence typing (MLST) allow monitoring and aid in the control of outbreaks. The high number of relevant genes makes multiple PCR and sequencing reactions necessary in order to characterise an isolate. PCR, though, suffers the risk of cross-contamination and the number of targets that can be analysed is limited. Intensified surveillance efforts and new outbreaks rapidly increase the need for automated testing of an larger number of isolates in a fast, affordable and exact manner. Our microarrays meet this need, allowing for simultaneous detection of a multitude of different targets. We have combined the advantages of mass produced high quality microarrays, an amplification and detection strategy with non-fluorescent labels and a highly affordable analysis and data mining software within the ArrayMate® platform. Starting from a single colony of an overnight culture, the system allows the detection of about 180 target genes, including virulence- and resistance-associated genes, and typing markers such as SCCmec, agr and capsule type. This information is used to automatically assign isolates to known clonal groups. In a microtiter-plate format, up to 96 isolates can be processed simultaneously.