The identification of Mycobacterium tuberculosis genes specifically expressed during infection is a key step in understanding mycobacterial pathogenesis. Such genes most likely encode products required for survival within the host and for progressive infection. Recent advances in mycobacterial genetics have permitted the development of new techniques and the adaptation of existing methods to analyse mycobacterial in vivo gene expression and virulence. This has revealed a subset of M. tuberculosis genes that are differentially expressed during infection and has demonstrated that a number of components contribute to the virulence of the organism. This information is expected to provide new strategies to prevent tuberculosis infection, new targets for antimicrobial therapy and new insights into the infectious process.