Food contamination from natural or anthropogenic sources poses severe risks to human health. It is now largely accepted that continuous exposure to low doses of food Toxins such as mycotoxins, phycotoxins can be related to several chronic diseases, including some type of cancer and serious hormonal dysfunctions. Contemporary analytical methods have the sensitivity required for contamination detection and quantification, but direct application of these methods on real samples can be rarely performed because of matrix complexity. Thus, selective analytical methods, relying on intelligent functional materials are needed. Recent years have seen the increasing use of molecular imprinted polymers in contaminant analysis in food because these materials seem to be particularly suitable for applications where analyte selectivity is essential. It offers several advantages to the agrofood industry in areas such as analysis, sensoring, extraction, or preconcentration of components. It has the potential of becoming a tool for acquiring truly simple, rapid, and robust direct measurements.