Many bacterial pathogens form cellular agglomerations known as biofilms, which considerably limit the success of both antibiotic treatment and the human immune defense. To gain insight into the pathophysiology of the leading nosocomial pathogen, Staphylococcus epidermidis, we analyzed the genome of biofilm-forming S. epidermidis, constructed a microarray representing its entire transcriptome, and performed expression profiling of an S. epidermidis biofilm. Gene-regulated processes in the biofilm led to a nonaggressive and protected form of bacterial growth with low metabolic activity, which is optimally suited to guarantee long-term survival during chronic infection. A class of peptides known as phenol-soluble modulins, which combine proinflammatory activity with a putative role in detachment of biofilms, evolved as potential key determinants controlling the switch between aggressive and quiescent modes of infection. Our data suggest that S. epidermidis adjusts its lifestyle to varying requirements during colonization and infection by means of an expansive change of gene expression. The observed physiological characteristics of the biofilm mode of growth—in particular, the contribution of surfactant-like peptides—might serve as a model for a variety of biofilm-forming pathogens.