This review presents natural products from cyanobacteria. Several classes of secondary metabolites are highlighted. Toxic metabolites from these prokaryotic photosynthetic organisms include compounds such as microcystin, anatoxin and saxitoxin, which display hepatotoxicity and neurotoxicity. Their potential as drugs in cancer therapy is discussed based on the cryptophycin class of potent cytotoxic agents. The next part of this review highlights iron chelators from cyanobacteria, including schizokinen, synechobactin and anachelin. The biogenesis of anachelin is investigated as its mechanism of iron acquisition. Several indole alkaloids are then reviewed, from simple carbolines such as bauerines and nostocarboline to complex polycyclic structures such as hapalindole, welwitindolinone and ambiguine. The latter compounds present fascinating structure combined with powerful bioactivities and interesting biogenetic pathways. In the last part, protease inhibitors from cyanobacteria are discussed (cyanopeptolins, micropeptin and oscillapeptin) and their structure/activity relationships and selectivity for trypsin / chymotrypsin are presented. All these examples highlight the large structural variety of cyanobacterial metabolites combined with powerful biological activities. Cyanobacteria can thus be considered a prime source both for novel bioactive compounds and for leads for drugs.