Abstract The toxins of cyanobacteria include potent neurotoxins and hepatotoxins. Deaths after exposure by ingestion of cyanobacterial cells and toxins from freshwater sources have been reported. The hepatotoxins are cyclic peptides, which comprise microcystins (MC) and nodularin (NOD), and they cause poisonings with an established syndrome of human and animal illnesses. The identification and determination of these hepatotoxic peptides are challenges for analytical chemists. Methods based on solid phase extraction and size exclusion chromatography are available for the clean up of raw extracts. Both principles are also used for the enrichment of MC from low contaminated sample material. The separation of MC is achieved by high-pressure liquid chromatography methods with ultraviolet (UV) detection or mass spectrometric detection. The unambiguous identification of MC not available as standards is possible by mass spectrometry (MS) or, under optimal conditions, by UV spectrometry using diode array detection. To date, 60 different MC and four NOD have been described, but new compounds are frequently identified. Therefore, powerful tools for the elucidation of the structure of unknown MC are an important need. In addition to classical methods for structure elucidation (e.g. nuclear magnetic resonance spectrometry), microwave-assisted hydrolysis of cyclic peptides followed by enantio-selective determination of the amino acid profiles can be used. More recently, MS with collision-activated dissociation has become an important tool for obtaining structure information. The present paper discusses the advantages and disadvantages of the various analytical techniques used for monitoring of cyanobacteria in lakes, optimized or developed at the Institute of Nutrition, Jena, Germany. A pathway for handling MC-containing samples with regard to different analytical tasks (i.e. the identification and elucidation of structure followed by qualitative and quantitative determination) is proposed.