A representative panel of 50 European MRSA isolates was subjected to genotype analysis by fluorescent amplified-fragment length polymorphism (FAFLP) and by macrorestriction pulsed-field gel electrophoresis (PFGE). Each isolate had a unique profile with FAFLP. To model genetic relationships within the continuing MRSA epidemic, cluster analysis of FAFLP data was made, revealing nine clone complexes of MRSA. Most of these were also found by PFGE. A number of isolates had FAFLP profiles significantly different from others, and might represent emerging epidemic strains. FAFLP analysis proved particularly suitable for surveillance of the MRSA epidemic at national and international levels.