Information on the relatedness of isolates causing repeated meticillin-resistant Staphylococcus aureus (MRSA) bacteraemia is limited. An observational study of 177 patients with MRSA bacteraemia, admitted to the emergency department of National Taiwan University Hospital, was conducted from January 2001 to June 2006. Among these patients, 28 had a previous episode of MRSA bacteraemia and 59 died during the index episode of bacteraemia. Until December 2007, among the 118 patients who survived the index episode (101 without previous bacteraemia and 17 with previous bacteraemia), 24 (20.3%) had repeated MRSA bacteraemia. The duration from discontinuation of antimicrobial therapy to repeat episodes was in the range 35–854 days (median 86 days). Eight patients (33.3%) died as a result of the second bacteraemic episode. Clinical characteristics associated with repeated bacteraemia included the diagnosis of infective endocarditis and active malignancy. Pulsed-field gel electrophoresis and multilocus sequence typing analysis were performed for 32 pairs of available isolates recovered from patients with repeated bacteraemia and revealed that 29 of them (90.6%) were genetically closely-related strains. The majority of patients with repeated MRSA bacteraemia had recurrent infections and a high mortality rate.