Mycotoxins are toxic fungal products that are produced when fungi grow in human and animal foods. A large number of food and beverage items can be contaminated with mycotoxins. Exposure to mycotoxins causes disease in humans and animals. Recent studies using biomarkers of exposure, internal dose, and adverse effects have shown that mycotoxins are underappreciated as a cause of disease. Some mycotoxins cross the placenta and are present in the fetus at birth and others are excreted in milk. Some mycotoxins cause neoplasia (cancer) in humans and animals and others cause kidney and neurological diseases. This chapter reviews the toxicokinetics, metabolism, and effects of mycotoxins in humans and other animals. It also discusses the biomarkers that are used and that have potential to be used in the diagnosis of mycotoxicoses, and that can be used to better understand the provenance of diseases caused by mycotoxins.