The availability of complete genome sequences of more than 160 pathogenic and non-pathogenic bacteria is facilitating the understanding of evolution of bacterial virulence. Comparative genomics revealed that most pathogens have a relative by stable core genome, encoding factors essential for growth in a specific environment and a flexible gene pool, encoding virulence traits, resistance determinants and genes that confer gene-mobility such as transposons, integrases and insertion sequences. The flexible part of the genome often determines the virulence of a particular organism. This concept originally developed for Enterobacteriaceae is now being proven also for gram-positive pathogens such as staphylococci, streptococci and enterococci. For example, pathogenic staphylococci are now the most common cause of nosocomial infections. It is assumed that the enormous genome plasticity of staphylococci is the basis for the rapid adaptation of staphylococci in the highly selective environment of hospitals. The genome of pathogenic staphylococci consists of a complex mosaic of larger regions which have been acquired by horizontal gene transfer. Remarkably, mobile genetic elements such as resistance and pathogenicity islands, bacteriophages, IS-elements, plasmids, and transposons are widespread among clinical isolates. In this review, we summarise the recent results from comparative genomics studies of selected gram-positive bacterial pathogens and discuss the implications of these studies for the evolution of bacterial pathogenicity.