The red pigmentation of Fusarium graminearum and related species that cause stem and head blight of cereals is due to the deposition of aurofusarin in the cell walls. To determine the importance of this polyketide for fungal physiology and pathogenicity, aurofusarin deficient mutants were produced by random and targeted mutagenesis of F. pseudograminearum and F. graminearum. We show that a gene cluster, including the F. graminearum PKS12 gene, is responsible for the biosynthesis of aurofusarin. Three F. pseudograminearum aurofusarin deficient mutants were disrupted in a region upstream from a gene with sequence homology to the aflatoxin regulatory gene aflR. Comparative PCR analyses of the aurofusarin gene cluster in F. graminearum, F. culmorum, and F. pseudograminearum show conserved organization and expression analyses detected no PKS12 transcripts in any of the mutants. To confirm that PKS12 encodes the precursor for aurofusarin, targeted mutagenesis was carried out in F. graminearum. All disruptants showed an albino phenotype. The DeltaPKS12 mutants have higher growth rate and a 10-fold increase in conidia production compared to the wild type. Aurofusarin does not appear to aid in radiation protection and all the mutants are fully pathogenic on wheat and barley. HPLC analyses of aurofusarin deficient mutants confirm the absence of aurofusarin and show an increase in the level of the mycotoxin zearalenone.