The chapter provides a comprehensive examination of the concept of secondary metabolites, encompassing discussions on various classification systems for these compounds, and an assessment of the available data management tools related to secondary metabolites. The main and most studied toxic and nontoxic secondary metabolites produced by cyanobacteria are described. Toxic metabolites are interpreted from the point of view of the primary target on which they act, while nontoxic metabolites are interpreted from the point of view of the biological role they play in cyanobacteria cells. For both categories, the possibility of practical application is being considered. Much attention is paid to cyanobacterial cytotoxins, which are promising substances in terms of creating drugs for the treatment of various forms of cancer. The chapter emphasizes the value of cyanobacteria as sources of valuable products, as well as their toxic potential in relation to other living organisms.