The high incidence of infection in Dublin hospitals caused by non-typable strains of methicillin- and gentamicin-resistant Staphylococcus aureus (MGRSA) has created an important epidemiological problem as conventional methods of sub-dividing these organisms have not been useful. This report describes a novel approach to the typing and analysis of MGRSA strains, particularly non-typable isolates, by comparing restriction endonuclease HindIII digest patterns of total cellular DNA; and by using Southern hybridization analysis to detect size variations or polymorphisms in restriction endonuclease cleavage fragments within small regions of the chromosome. Non-typable MGRSA strains and isolates belonging to two phenotypically related groups of phage-type 77 and 77/84 strains were readily subdivided on the basis of molecular size differences in high molecular weight DNA fragments generated by the enzyme HindIII. Restriction endonuclease fragment size polymorphisms were readily detected in many of the non-typable strains tested in hybridization experiments, and these were used for strain sub-division. Both techniques were useful tools for the separation of closely related MGRSA strains.