Methicillin-resistant Staphylococcus aureus (MRSA) is a well-recognized cause of hospital-acquired sepsis. We reviewed the clinical features of a new variant of community-acquired MRSA originally described from the Kimberley region of northern Western Australia (WA MRSA). This strain has become an increasing cause of community- and hospital-acquired sepsis at Royal Darwin Hospital (RDH) in the Northern Territory, especially in Aboriginal Australians from remote communities. Fifty percent of WA MRSA was community-acquired, with 76% in Aboriginals. Like the MRSA from eastern Australia (EA MRSA), WA MRSA commonly caused skin sepsis but was less likely to cause respiratory or urinary infections compared with EA MRSA. Twelve out of 125 (9.6%) WA MRSA and 7/93 (7.5%) EA MRSA infections were septicaemias. Septicaemia due to WA MRSA occurred in adult medical patients, especially those with temporary haemodialysis catheters, while EA MRSA septicaemia occurred throughout the hospital. Aboriginal people were more likely to develop both community- and hospital-acquired WA MRSA septicaemia [overall relative risk (RR) 12.3 (95% CI 3.7-40.7)]. Control of WA MRSA requires policies to reduce transmission in both hospitals and communities. Community-based control programmes need support for individual patient management, improved housing and hygiene, control of skin sepsis and appropriate use of antibiotics, especially in rural Aboriginal communities in northern Australia.