Staphylococcus aureus is an important human and veterinary pathogen that causes a wide variety of infections ranging from benign skin infections to life threatening diseases. Recently, important changes in the epidemiology have been reported demonstrating that S. aureus, and particularly its methicillin-resistant variant, is now recognized as a ubiquitous pathogen responsible for both, hospital- and community-acquired infections. In these settings, the bacterium is responsible for various acute or chronic diseases and shows particular ability to adapt its metabolism to major environmental changes. Despite the fact that S. aureus infections are common worldwide, the factors triggering the different steps of infection (colonization, expression of virulence factors, invasion of host tissues, and persistence in hostile environments) are not fully characterized. Over the last decade highly parallel methods of analysis led to the release of whole genome sequences of numerous pathogenic bacteria. These efforts coupled to the parallel improvements of proteomic procedures permitted to study S. aureus transcriptome or proteome at the organism level. This now provides a sound basis for a comprehensive understanding of bacterial metabolism, adaptability to environment and pathogenicity mechanisms. This review summarizes the impact of proteomic on our comprehension of S. aureus virulence and pathogenesis.