Recent decades have seen the global emergence of meticillin-resistant Staphylococcus aureus (MRSA), causing substantial health and economic burdens on patients and health-care systems. This epidemic has occurred at the same time that policies promoting higher patient throughput in hospitals have led to many services operating at, or near, full capacity. A result has been limited ability to scale services according to fluctuations in patient admissions and available staff, and hospital overcrowding and understaffing. Overcrowding and understaffing lead to failure of MRSA control programmes via decreased health-care worker hand-hygiene compliance, increased movement of patients and staff between hospital wards, decreased levels of cohorting, and overburdening of screening and isolation facilities. In turn, a high MRSA incidence leads to increased inpatient length of stay and bed blocking, exacerbating overcrowding and leading to a vicious cycle characterised by further infection control failure. Future decision making should use epidemiological and economic evidence to evaluate the effect of systems changes on the incidence of MRSA infection and other adverse events.