Recent advances in both technology and molecular biology have opened the way to the development of high-throughput techniques. DNA microarrays benefited from these determinant efforts and are now becoming conventional methods. Surprisingly, the most complicated organisms (i.e. eukaryotes) were the first targets of microarray-based experiments. Completion of sequencing projects for numerous bacterial genomes has recently enabled the design of non-model prokaryotic microarrays. Several important social fields will benefit from transcriptomic analysis of bacteria, such as human and veterinarian medicine, the food industry, or bioremediation. This review presents the current status of microbial studies using microarrays and describes limitations and caveats encountered in microarray design, experimental techniques, exploration and analysis of large data sets, as well as nomenclature issues that currently challenge microarray users.