Mycotoxins are produced as secondary metabolites by various species of filamentous fungi, and may affect many agricultural crops and products. The potential health risks associated with these chemical compounds mean that significant attention has been given to their detection and control. However, most study has so far been dedicated to mycotoxin contamination of agricultural crops such as cereals, with less attention given to cocoa. This chapter presents an overview of the current understanding of mycotoxin contamination of cocoa. The main groups of mycotoxins are discussed, followed by a summary of three methods of detection. There follows an explanation of various methods of controlling mycotoxins in cocoa, including recommendations at the stages of production, processing and fermentation and discussion of attempts to decontaminate infected crops. It is concluded that there is a need for more research into the different mycotoxins affecting cocoa and methods of reducing their presence and impact.