Bacteria are faced with a diversity of environmental stresses that include high salt concentrations, heavy metals and pH fluctuations. Adaptation to resist such stresses is a complex phenomenon that involves global pathways and simultaneous acquisition of multiple unrelated properties. During the last 3 years, the development of new technologies in the field of molecular biology has led to numerous fundamental and quantitative in vitro and in vivo evolutionary studies that have improved our understanding of the principles underlying bacterial adaptations, and helped us develop strategies to cope with the health burden of bacterial virulence. In this review, the authors discuss the evolution of bacteria in the laboratory and in human patients.