An overview is given of the biological origin of phycotoxins, as well as their chemical characteristics. Major poisoning types are described and examples of poisoning events are given to illustrate the importance of the phenomenon to both shellfish consumers and the shellfish producing industry. The characteristics of phycotoxins as natural products, the lack of predictability of their occurrence, economic drivers and the freshness of shellfish consumed in many countries result in a number of requirements for methods to be used in the efficient detection of these compounds. Subsequently, the performance of mouse bioassays and mass spectrometry as detection tools are compared for examples from Irish and French monitoring programmes to assess the usefulness of qualitative and quantitative tools in official control, and their fitness for purpose compared with the requirements. The final part of the paper critically reviews methods available for the end-product and official control of shellfish toxins and their use in screening and confirmatory approaches in monitoring. Recent expert consultations on the methodology for phycotoxins at European and global level are summarised and recommendations are made for future progress in this area.