Rapid detection and typing of methicillin-resistant Staphylococcus aureus are important components of infection control programmes. A protocol is described that enables sequencing of the spa gene fragment directly from a multiplex PCR targeting the clinically relevant mecA, pvl and spa genes, resulting in high-throughput characterisation of S. aureus. Implementation of the method in the Danish national reference laboratory has markedly reduced the use of reagents and the requirement for hands-on time, and has also provided fast typing results. In addition, the method reduces the risk of sample mishandling.