In order to better understand the mechanism of daptomycin resistance, we generated a daptomycinnonsusceptible derivative strain, strain 103ءd1 (MIC ؍ 3.0 g/ml), by in vitro exposure of methicillinresistant Staphylococcus aureus strain N315⌬IP (MIC ؍ 0.5 g/ml) to daptomycin. We also obtained a daptomycin-susceptible phenotypic revertant strain, strain 103ءd1-10 (MIC ؍ 1.0 g/ml), by passaging 103ءd1 in drug-free medium for 10 days. The resultant triple-isogenic strains were analyzed for their phenotypes and gene expression by microarray analysis. No significant differences in the membrane fluidities of 103ءd1 and 103ءd1-10 compared to the membrane fluidity of N315⌬IP were observed. Resistant strain 103ءd1 had the highest membrane potential, followed by strains 103ءd1-10 and N315⌬IP. The vancomycin and teicoplanin MICs also increased. Teichoic acid genes (tagA, tagG), mprF encoding lysyl-phosphatidylglycerol, and cls encoding cardiolipin synthase were downregulated in 103ءd1 and 103ءd1-10. The vraF and vraG genes, which encode ATP binding cassette transporter proteins, were upregulated in 103ءd1. The vraSR two-component regulatory system was upregulated, and electron microscopy revealed that the cell wall of 103ءd1 was significantly thicker than that of the parental strain. Taken together, daptomycin exposure selected a daptomycin-nonsusceptible strain with a phenotype similar to that of heterogeneous vancomycin-intermediate S. aureus and a transcription profile that partially overlapped that of heterogeneous vancomycin-intermediate S. aureus.