Several microorganisms capable of chemolithotrophic growth on carbon monoxide with concomitant production of hydrogen have been isolated from a variety of different environments. Genome analysis of some of these microorganisms has revealed similar gene clusters that code for the subunits of carbon monoxide dehydrogenase complexes, with cooA functioning as both a CO sensor and transcriptional regulator. Carboxydothermus hydrogenoformans, was chosen as a model organism for gene expression studies, to help gain an understanding of the novel metabolic capabilities of carboxydotrophs. Based on the C. hydrogenoformans genome, a targeted oligonucleotide microarray was developed containing 463 of the 2,646 putative protein coding genes (17.5% of genes). All genes involved in carbon monoxide metabolism were included, plus genes for transcriptional regulation, energy transduction, metal utilization and transport, motility, and the citric acid cycle. Individual 5'-exonuclease real-time RT-PCR assays targeting five homologs of cooS, the catalytic subunit of the CO-dehydrogenase (CODH) enzyme complex, and the two homologs of cooA, were also developed. Changes in gene expression were evaluated relative to various concentrations of yeast extract present in the growth medium and relative to CO concentration in the headspace. Genome analysis identified a variety of cooA binding sites distributed throughout the CODH complexes, allowing for differential expression of genes contained within a single putative operon.