Two groups of clinical Staphylococcus aureus isolates were examined by molecular typing methods. Detailed protocols for the technical procedures are described. By means of plasmid DNA profiles, plasmid DNA restriction enzyme digestion, as well as whole-cell DNA endonuclease digestions subjected to conventional agarose gel electrophoresis and pulsed-field gel electrophoresis, eight methicillin-susceptible S. aureus strains from three patients segregated into three different groups. Consecutive isolates from the same patient revealed identical fingerprints. Generally, good agreement between different molecular typing methods also was achieved in the investigation of 28 methicillin-resistant isolates. However, compared to whole-cell DNA restriction endonuclease analysis, plasmid DNA profiling (all but one strain had detectable plasmid DNA) showed a somewhat greater discriminatory ability. The techniques evaluated were reproducible and relatively easy to perform and provided valuable tools for studying the epidemiology of S. aureus in hospitals.