The arrival of the post-genomic era has allowed the regulation of every gene or protein of an organism to be studied at once using microarrays for transcriptomic studies, proteomics to analyse gene products, and metabolomics to study the complete complement of products and intermediary metabolites produced by a single person or a single organism. Too often the results of such enterprises are disappointing either because many of the products cannot be identified, or because they are products of genes of unknown function. Success is far more likely to be achieved if the organism to be exploited is thoroughly understood at the levels of genome organisation, regulation, physiology and biochemistry. Typical questions asked in biotechnology and the biopharmaceutical industries include what genes are expressed ? or not expressed ? when recombinant protein production is induced: can they be manipulated to provide a more productive host; and how do successful pathogens survive in the human body when exposed to oxygen starvation or chemical attack by host defence mechanisms. Examples are given of how whole genome microarray data can reveal mechanisms used by bacteria to survive when they are starved of oxygen; what genes are turned on in response to host defence mechanisms such as nitrosative attack; and how pathogens repair damage inflicted by the host defence mechanisms. Striking similarities and fascinating differences are revealed between two major groups of pathogenic bacteria: enteric bacteria that are able to adapt to life both inside and outside an animal host, and the obligate human pathogen, Neisseria gonorrhoeae. Proteins are identified that provide possible targets for biopharmaceutical intervention, and hence illustrate the potential value of whole-genome transcriptomic approaches to biotechnology.