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An oligonucleotide array of more than 250,000 specific probes representing two complete bacterial genomes including the 1,743 open reading frames of Haemophilus influenzae, and the 1,969 open reading frames of Streptococcus pneumoniae has been designed. When hybridised against labelled genomic DNA, all genes were detected and more than 96% of the signal intensity values were within a factor of three of the mean. For transcript imaging, microarrays were hybridised against total RNA populations quantitatively represented by labelled cDNAs. The measurements of transcript abundance for all genes were shown to be sensitive, specific, quantitative and reproducible. Nearly 85% of all S. pneumoniae mRNAs were found expressed during in vitro exponential growth. Identification of regulons important for S. pneumoniae entry into the stationary phase has been used to validate the approach. We will show, for the first time, how a genome-wide transcriptional analysis is applied to bacterial genomes and is being used to identify signal transduction regulatory networks, and to profile antibiotic compounds.