Topical mupirocin is widely used for the decolonization of methicillin-resistant Staphylococcus aureus (MRSA) carriers. We evaluated the capacity of various MRSA clonotypes to develop mutations in the ileS gene associated with low-level mupirocin resistance. Twenty-four mupirocin-sensitive MRSA isolates from a variety of genotypes (determined by multilocus variable number of tandem repeats assay) were selected. Mupirocin MICs were determined by Etest. The isolates were then incubated in sub-inhibitory concentrations of mupirocin for 7-14 days. Repeat MIC determination and sequencing of the ileS gene were then performed. Doubling times of isolates exposed and unexposed to mupirocin were compared. We found that exposure to mupirocin led to rapid induction of low-level resistance (MICs 8-24 µg/ml) in 11 of 24 (46%) MRSA isolates. This phenomenon was observed in strains with diverse genetic backgrounds. Various mutations were detected in 18 of 24 (75%) MRSA isolates. Acquisition of mutations appeared to be a stepwise process during prolonged incubation with the drug. Among five low-level resistant isolates with the highest MICs, four tested sensitive after incubation in the absence of mupirocin but there was no reversion to the susceptible wild-type primary sequence. Resistance was not associated with significant fitness cost, suggesting that low-level mupirocin-resistant MRSA strains may have a selective advantage in facilities where mupirocin is commonly used. Our findings emphasize the importance of the judicious use of this topical agent and the need to closely monitor for the emergence of resistance.