Cyanobacteria (blue-green algae) produce a wide range of low molecular weight metabolites that include potent neurotoxins, hepatotoxins, and cytotoxins. The accumulation of such toxins in freshwaters, and in brackish and marine waters presents hazards to human and animal health by a range of exposure routes. A review is presented of developments in the detection and analysis of cyanobacterial toxins, other than bioassays, including application of physicochemical, immunoassays, and enzyme-based methods. Analytical requirements are considered with reference to recently derived guideline levels for the protection of health and to the availability, or otherwise, of purified, quantitative cyanobacterial toxin standards.