Isoprenol quinone identification is used to complement fatty acid composition, polar lipid patterns and, in some cases, determination of the peptidoglycan type as part of the chemotaxonomic characterization of prokaryotes. Although the results are not usually discriminatory at the species level, they provide valuable data at higher taxonomic levels. We will give some examples of the value of the isoprenoid quinone analysis and describe the methods that can be used in almost all laboratories, requiring simple chemical techniques for extraction and purification and, in most cases, only a high-performance liquid chromatograph fitted with a reverse phase column and a UV detector, which are available in most scientific institutions. The information obtained is important for taxonomic purposes and adds to our knowledge of the groups of organisms we are working with. © 2011 Elsevier Ltd.