The Cnidaria are simple organisms that have remarkable physiological features susceptible to microscopic investigation. As a group they produce cnidae, the most complex intracellular organelles known, form symbioses with a range of unicellular algae, contain mucocytes that account for a very substantial fraction of their body mass, and form complex skeletal structures of calcium carbonate. This review summarises contributions dealing with the distribution and localisation of metals of physiological and pathological importance within soft tissues and skeletons. Whilst there have been detailed studies of microscale metal distribution, using X-ray microanalysis, in the stinging organelles or cnidocysts and in mucocytes, other cells such as symbiotic algae and the epithelial cells have received little attention. In the skeleton-producing scleractinian corals X-ray microanalysis has provided tenuous, but persistent, evidence of Ca associated with intracellular vesicles or granules in the skeletogenic epithelium, even though the investigations were technically limited. These observations may be germane to the intriguing and intransigent problem of the mechanism of coral calcification. Metal localisation in coral skeleton at the resolution of annual growth rings has been concerned with the validity of Sr/Ca and Mg/Ca ratios as thermometers for paleoclimatic studies. It is not clear whether these ratios are influenced primarily by environmental or biological parameters. Microscale analyses by X-ray microanalysis and ion microprobe indicate a much greater variability of metal ratios which suggests biological control of metal deposition. New data are provided on the elemental composition, measured by X-ray microanalysis, of cells and cell compartments in the coral Galaxea fascicularis and zooxanthellae in the anemone Aiptasia sp. New information is also presented on changing Ca/Sr ratios at the skeletal interface in Galaxea fascicularis.