Staphylococcus aureus small-colony variants (SCVs) are a naturally occurring, slow-growing subpopulation with distinctive phenotypic characteristics and pathogenic traits. Many reports support a pathogenic role for SCVs in patients with persistent and/or recurrent infections. Multiple features of SCVs are similar to anaerobically grown S. aureus. Sequence analyses led to the hypothesis that a regulator protein called Rex (redox sensing regulator) senses oxygen limitation by responding to high levels of NADH. In this study, full-genome DNA microarrays were used to analyze the transcriptome of a ∆rex mutant. Comparing the expression profile of the ∆rex mutant to that of its parental strain at different time points, the accessory gene regulator (agr), genes for capsular polysaccharide synthesis (cap5A, cap5B, cap5D, cap8E), a gene of a fibronectin-binding protein homologue, and genes of different Na⁺/H⁺ antiporters were found to be significantly down-regulated. In contrast, genes for a cell division and morphogenesis-related protein (scdA), superoxide dismutase (sodM), the immunodominant antigen B (isaB), L-lactate dehydrogenase (lctE), a formate acetyltransferase activating enzyme (SA0219) and for the alcohol-acetaldehyde dehydrogenase (adhE) were shown to be significantly up-regulated. The large overlap between the Rex regulon and the transcriptome analyzed in a hemB mutant displaying the phenotype of clinical SCVs suggest that at least part of the SCV phenotype may arise from changes in Rex regulation of the anaerobic regulon.