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Objectives: Staphylococcus aureus is an important nosocomial pathogen that produces various extracellular toxins. Epigallocatechin gallate (EGCg) is a polyphenol that is abundant in green tea. EGCg displays strong antibacterial activity against Gram-positive bacteria. The effect of EGCg on gene expression by S. aureus was investigated to clarify the mechanism underlying its antibacterial action. Methods: Microarray analysis was performed on S. aureus treated with or without 500 mg/L EGCg. Differentially expressed genes were identified and their changes at the transcription level were confirmed using real-time quantitative polymerase chain reaction (qPCR). The membrane potential of cells treated with or without EGCg were observed under fluorescence microscopy. Results: Microarray analysis revealed that EGCg treatment of S. aureus resulted in increased and decreased transcription of 75 and 72 genes, respectively. Increased transcription exceeding 1-log2-fold change of genes related to membrane transport included gntP, gntK, rumA, SAOUHSC_02723, SAOUHSC_01311, and vraS. Decreased transcription was observed in genes involved in toxin production and stress response (hlgA, SAOUHSC_01110, hly, hlgB, efb, and hlgC). All changes in transcription were confirmed using real-time qPCR. The membrane potential of S. aureus treated with 500 mg/L EGCg markedly decreased, indicating that EGCg damaged the cell membrane. Conclusions: S. aureus increases the transcription of genes involved in membrane transport to recover membrane function. EGCg can potentially serve as a natural antibacterial agent to control the growth and toxin production of S. aureus.