A remarkable feature of filamentous fungi is their ability to produce small yet structurally complex and often bioactive natural products. In this mini-review, we cover advances in the research on fungal secondary metabolites, particularly mycotoxins, and focus on biosynthetic aspects as well as on the complex regulatory mechanisms which control the expression of biosynthetic genes. We also highlight the increasing impact of genomics and transcriptomics, which help explore the realm of secondary metabolism of fungi.