Many methods have been described for the detection of methicillin-resistant Staphylococcus aureus (MRSA), but the homogeneous or heterogeneous expression of methicillin resistance affects the reliability of those methods. This study demonstrates that close association between methicillin-susceptible S. aureus (MSSA) and MRSA strains in the host colonisation site can present additional problems for the detection of MRSA in clinical laboratories, which may contribute to failure in the control of MRSA infection in hospital. Worse, this association may also account for the emergence of MRSA during antibiotic therapy.