Eradication of methicillin-resistant Staphylococcus aureus (MRSA) colonisation may prevent transmission of strains between patients and reduces the risk of clinical infection. Colonisation of the throat is associated with prolonged carriage and is more difficult to eradicate. An open randomised study was conducted to evaluate two eradication protocols. Patients with pharyngeal carriage of MRSA were enrolled at six Swedish centres during 4 years. One treatment group received oral rifampicin and either clindamycin or trimethoprim/sulfamethoxazole (SXT) for 7 days in combination with nasal mupirocin. Patients in the other group were treated with nasal mupirocin only. Patients in the same household were randomised together. Both groups followed a hygiene protocol including chlorhexidine washing. Cultures from the nares, perineum and throat were taken at baseline and then at 2 weeks, 2 months and 6 months after the end of treatment. A total of 28 patients received rifampicin-based systemic antibiotics and 24 subjects received mupirocin only. At follow-up 6 months after the end of treatment, 61% of patients and 50% of households in the systemic antibiotics group had culture results negative for MRSA. Significantly less patients (12%) and households (10%) became decolonised in the group receiving topical treatment only. A combination of rifampicin and either clindamycin or SXT was more effective in eliminating pharyngeal MRSA carriage compared with topical treatment with mupirocin only.