The dimorphic phytopathogenic fungus Ustilago maydis encounters different environments during its life cycle. As free-living unicellular haploid cell, the fungus must compete with other microorganisms for space and nutrients. As a pathogen, it also has to withstand the defense reactions of its host plant corn and to subvert the plant metabolism for its own purposes. During these interactions small molecules produced by the fungus serve important functions in the communication with its host and other organisms. The genome sequence of U. maydis makes it possible to deduce the full inventory of enzymatic functions that are involved in the production of these secondary metabolites. Although the fungus is known to secrete interesting small molecules the genome contains surprisingly few genes involved in the biosynthesis of polyketides (PKS) and non-ribosomal peptide synthetases (NRPS). Additional genes predicted to be part of secondary metabolism are located in subtelomeric regions suggesting that they are subject to high genetic and genomic variation. Here we review the pathways for the production of extracellular glycolipids that serve as biosurfactants, iron-chelating siderophores, tryptophan-derived indole pigments and indole acetic acid, the elucidation of which has greatly profited from the availability of the U. maydis genome sequence.