The development of advanced molecular diagnosis for the critical toxigenic Fusarium species is considered in this review. The specific topics discussed are (1) isolation of mating type genes of Gibberella complex, (2) molecular detection of Fusarium-producing fumonisins, (3) molecular detection of Fusarium-producing trichothecenes and enniatins. Particular attention is given to the development of PCR assays for genes involved in the toxin biosynthesis that would permit the early detection of Fusarium species-producing toxins and potentially even reveal which particular toxin may be present within a food or feed product. Most of these data have been obtained within the 'De-Tox Fungi' project supported by the European Commission (QLK1-CT-1998-01380).