Microbiology has entered the postgenomic era and it is clear that bacterial typing should aim to be based on analysis of complete genomes. Although complete genome sequencing for epidemiological typing remains unrealistic for the present, microarrays that provide information on gene content are now becoming available. Microarrays comprised of several thousand probes on glass slides can now be manufactured in the laboratory using robotic arrayers. The gene probes are either PCR products or synthetic oligonucleotides that can be irreversibly attached to a reactive glass surface. The target nucleic acids to be hybridized to the probe array are tagged with fluorescent dyes. Relative probe hybridization signals can be measured when two or more different preparations are labeled with distinguishable fluorophores. Microarrays that include probes for every gene within a genome provide excellent comparative data, although a focus on variable genes may be more useful for typing purposes. Composite arrays of variable genes are under development.