This review presents several types of metabolites produced by the most common fungal pathogens and their roles in fungal pathogenesis. Toxic metabolites from toxigenic fungi include compounds such as aflatoxins, trichothecenes, ochratoxins, fumonisins, zearalenone and ergot alkaloids, which display hepatotoxicity, nephrotoxicity, neurotoxicity and genotoxicity. The ability of fungi to produce and elaborate hydrolytic enzymes is associated with virulence of several pathogenic fungi. The biogenesis of siderophores is investigated as it is a mechanism of iron acquisition. In particular, these metabolites act as iron chelators and storage compounds to support pathogenic fungi to survive in mammalian hosts whose iron homeostasis is strictly regulated and prevent the formation of free radicals which are formed by free iron. Melanins clearly promote infectivity in a number of species of fungal pathogens. They interfere with oxidative metabolism of phagocytosis making the fungus relatively resistant to phagocyte attack. Several metabolies such as pullulan, mannitol, β-(1,3)-glucan, hem-binding proteins, estrogen-binding proteins, farnesol, agglutinin-like sequence proteins, glucuronoxylomannan and others also have advantages in fungal pathogenicity. The identification of fungal metabolites involved in pathogenesis, and recognition of mechanisms of pathogenesis may lead to development of new efficient anti-fungal therapies.