Continuous exposure to low doses of myco- and phyco-toxins poses severe risks to human health. 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 because these materials seem to be particularly suitable for applications where analyte selectivity is essential. In this review, several applications of molecular imprinted polymers in myco- and phyco-toxin contamination analysis will be discussed.