The complete sequence of the bacterial genomes provides new perspectives for the study of gene expression and gene function. By the combination of the highly sensitive 2-dimensional (2D) protein gel electrophoresis with the identification of the protein spots by microsequencing or mass spectrometry we established a 2D protein index of Bacillus subtilis that currently comprises almost 400 protein entries. A computer-aided evaluation of the 2D gels loaded with radioactively-labelled proteins from growing or stressed/starved cells proved to be a powerful tool in the analysis of global regulation of the expression of the entire genome. For the general stress regulon it is demonstrated how the proteomics approach can be used to analyse the regulation, structure and function of still unknown regulons. The application of this approach is illustrated for the sigmaB dependent general stress regulon. For the comprehensive description of proteins/genes belonging to stimulons or regulons it is generally recommended to complement the proteome approach with DNA array techniques in order to identify and allocate still undiscovered members of individual regulons. This approach is also very attractive to uncover the function of still unknown global regulators and regulons and to dissect the entire genome into its basic modules of global regulation. The same strategy can be used to analyse the regulation, structure and function of regulons encoding virulence factors of pathogenic bacteria for a comprehensive understanding of the pathogenicity and for the identification of new antibacterial targets.