Mycotoxins are fungal secondary metabolites that if ingested can cause a variety of adverse effects on both humans and animals, ranging from allergic responses to death. Therefore, exposure to mycotoxins should be minimized. A variety of physical, chemical, and biological methods have been developed for decontamination and/or detoxification of mycotoxins from contaminated foods and feeds. This overview details the latest developments in the biological control of both fungal infection and mycotoxin formation and describes the detoxification of many of the most important mycotoxins by microorganisms. This review also addresses the potential for use of microorganisms as mycotoxin binders in the gastrointestinal tract of both humans and animals, thereby reducing the potential deleterious effects of exposure to these toxins.