The development of microarrays for genome comparison and transcriptional profiling along with the public availability of several meningococcal genome sequences has promoted studies elucidating (i) intraspecific and interspecific genomic differences of members of the genus Neisseria, and (ii) the transcriptional response of meningococci to a variety of environmental stresses such as heat shock, iron starvation, serum treatment, and contact with eukaryotic cells. Furthermore, microarray-based finetyping of meningococci is in development. It will remain a difficult, but important, goal to identify sets of genes determining the virulence potential of hypervirulent meningococcal lineages in comparison with apathogenic ones. The recent identification of the meningococcal disease-associated island through the application of microarray analyses has been a step towards this aim. Transcriptional profiling of meningococci has brought about the compilation of large datasets, which also provide information about several regulons. Meningococcal microarray analysis has established a basis for studies clarifying the function of previously unknown genes, and has supported the identification of interesting vaccine candidates. However, harmonization of protocols and tools, as well as central databases are needed to foster the comparability of studies and the integration of knowledge.