In 2007 in The Netherlands, 30% of all human isolates of methicillin-resistant Staphylococcus aureus (MRSA) sent to the National Institute for Public Health and the Environment could not be typed by pulsed-field gel electrophoresis (non-typable (NT)-MRSA). Molecular characterisation of the NT-MRSA isolates revealed 27 different spa types and two distinct SCCmec types, type IV and V. All NT-MRSA isolates were closely related based on spa and multi-locus sequence typing and belonged to the ST398 lineage. The rapid increase of NT-MRSA (ST398) isolates over the last years shows the importance of this relatively new clonal lineage.