This paper reviews the early detection and prevention strategies which have been employed in Europe for the control of mycotoxin contamination of food in the context of a hazard analysis critical control point (HACCP) framework. The critical control points (CCPs) in the whole food chain where mycotoxins such as trichothecenes and ochratoxins are important have been identified. Ecological studies on the effect of environmental factors which are marginal for growth and mycotoxin production have been identified for Fusarium culmorum and F. graminearum (deoxynivlenol production), and for Penicillium verrucosum and Aspergillus ochraceus (ochratoxin production) in relation to cereal production and for A. carbonarius in relation to grapes and wine production (ochratoxin formation). To minimise the entry of these mycotoxins into the food chain, effective and rapid diagnostic tools are required to monitor the CCPs effectively. To this end the potential use of molecular imprinted polymers, lateral flow devices and molecular-based techniques for the rapid detection and quantification of the mycotoxigenic moulds or their toxins have also been developed.