Methicillin-resistant Staphylococcus aureus (MRSA) infection is an increasing threat to critically ill patients in many intensive care units. MRSA bacteraemia is an extreme form of MRSA infection and is a significant cause of morbidity and mortality. This case control study aimed to assess the risk factors and outcomes of MRSA bacteraemia compared to methicillin-susceptible Staphylococcus aureus (MSSA) bacteraemia. A total of 21 MRSA bacteraemia and 60 randomly selected MSSA bacteraemia episodes, admitted to the intensive care unit at Royal Perth Hospital between 1997 and 2007, were considered. There was a suggestion that hospitalisation within the preceding six months (P = 0.087) and residence in a long-term care facility (P = 0.065) were associated with a higher risk of MRSA bacteraemia. MRSA bacteraemia was more often treated with antibiotics to which the pathogen was not susceptible in vitro (38.1% vs 0%, P = 0.001), resulting in a longer duration of fever (median 7.0 vs 2.0 days, P= 0.009) and bacteraemia (mean 3.2 vs 0.6 days, P = 0.005) and a higher incidence of metastatic seeding of infection (52.4% vs 21.7%, P = 0.012) as compared to MSSA bacteraemia. While in-hospital mortality between MRSA and MSSA was similarly high (47.6% vs 38.3% for MRSA and MSSA respectively, P = 0.607), a significant proportion of the patients who had MRSA bacteraemia died within five years of hospital discharge (36.4%, hazard ratio 26.0, 95% confidence interval 1.90 to 356.7, P = 0.015). Infections contributed to 75% of the deaths after hospital discharge in patients who had an episode of MRSA bacteraemia. MRSA bacteraemia carries a much worse long-term prognosis than MSSA bacteraemia and that could be explained by recurrent MRSA infections and residual confounding.