Staphylococcus aureus is the most commonly isolated pathogen in respiratory tract secretions from young patients with cystic fibrosis (CF), and several treatment strategies are used to control the infection. However it is not known whether intensified treatment with antimicrobial agents causes eradication of S. aureus clones. We retrospectively determined the impact of intravenous (IV) antimicrobial agents on suppression and eradication of S. aureus clones. One thousand and sixty-one S. aureus isolates cultured from 2,526 samples from 130 CF patients during a two-year study period were subjected to spa-typing. Intervals between positive samples and occurrence of clone replacements were calculated in relation to courses of IV administered antimicrobial agents. Of 65 patients chronically infected with S. aureus, 37 received 139 courses of IV antimicrobial agents with activity against S. aureus (mean duration 15 days, range 6-31). Administration of IV antibiotics increased the time to next sample with growth of S. aureus: the mean interval between two positive samples was 68 days if IV treatment had been administered, in contrast to 49 days if no IV treatment had been administered (p=0.003). When S. aureus recurred in sputum after IV treatment, the isolate belonged to a different clone in 33 of 114 (29%) intervals, in comparison with 68 of 232 (29%) intervals where IV treatment had not been prescribed (OR=0.98, 95% CI=0.60; 1.61). In conclusion we show that two-week IV antimicrobial treatment can significantly suppress chronic staphylococcal infection in CF, but is not associated with eradication of persistent bacterial clones. This article is protected by copyright. All rights reserved.