Objective To evaluate microbiological effectiveness, that is, culture negativity of a non-blinded eradication protocol (Rx) compared with observation (Obs) in clinically stable cystic fibrosis participants with newly positive methicillin resistant Staphylococcus aureus (MRSA) cultures. Design This non-blinded trial randomised participants ages 4-45â €..years with first or early (≤2 positive cultures within 3â €..years) MRSA-positive culture without MRSA-Active antibiotics within 4â €..weeks 1:1 to Rx or Obs. The Rx protocol was: oral trimethoprim-sulfamethoxazole or if sulfa-Allergic, minocycline plus oral rifampin; chlorhexidine mouthwash for 2â €..weeks; nasal mupirocin and chlorhexidine body wipes for 5â €..days and environmental decontamination for 21â €..days. The primary end point was MRSA culture status at day 28. Results Between 1 April 2011 to September 2014, 45 participants (44% female, mean age 11.5â €..years) were randomised (24 Rx, 21 Obs). At day 28, 82% (n=18/22) of participants in the Rx arm compared with 26% (n=5/19) in the Obs arm were MRSA-negative. Adjusted for interim monitoring, this difference was 52% (95% CI 23% to 80%, p<0.001). Limiting analyses to participants who were MRSA-positive at the screening visit, 67% (8/12) in the Rx arm and 13% (2/15) in the Obs arm were MRSA-negative at day 28, adjusted difference: 49% (95% CI 22% to 71%, p<0.001). Fifty-four per cent in the Rx arm compared with 10% participants in the Obs arm remained MRSA-negative through day 84. Mild gastrointestinal side effects were higher in the Rx arm. Conclusions This MRSA eradication protocol for newly acquired MRSA demonstrated microbiological efficacy with a large treatment effect. Trial registration number NCT01349192.