A microarray, which covers most of the known relevant mycotoxin biosynthesis genes, has been developed. The microarray carries oligonucleotides of the fumonisin, the aflatoxin, the ochratoxin, the trichothecene (type A and B) and the patulin biosynthesis pathways. For trichothecene producing Fusaria the biosynthesis cluster of trichothecene producing Fusarium sporotrichioides (type A) and of Gibberrella zeae (type B, teleomorph of F. graminearum) have been spotted. The aflatoxin cluster carries oligonucleotides specific for Aspergillus flavus. The ochratoxin pattern is specific for ochratoxin A producing Penicillia, the fumonisin cluster is specific for G. moniliformis (teleomorph of F. verticillioides) and the patulin genes have been obtained from Penicillium expansum. The microarray is designed in a way that newly identified pathway genes can be added easily at any time. The microarray was used to detect the activation of all gene clusters under conditions conducive for mycotoxin biosynthesis. According to the results the obtained signals were specific under the hybridization conditions used and only insignificant cross-hybridizations occurred. The microarray was used to demonstrate differences in mycotoxin pathway gene expressions after growth on various media for trichothecene and ochratoxin A biosynthesis. It was used further to study and compare the expression kinetics of the trichothecene biosynthesis genes of Fusarium on different trichothecene supporting media. An expression pattern indicative for trichothecene biosynthesis could be identified.