A reliable and sensitive PCR assay to specifically detect trichothecene-producing Fusarium spp. in milling fractions and kernel tissue of naturally infected durum wheat is reported. Assays were based on a combination of primers derived from the trichodiene synthase and the â-tubulin genes. The occurrence of toxigenic Fusarium spp. in semolina and wheat tissue (grain ends, crease, pericarp, aleurone layer, germ and albumen) was detected, even for a weakly contaminated wheat sample. Penetration of toxigenic Fusarium spp. into the interior of durum wheat kernel was demonstrated for the Nefer variety, indicating that none of the tissue structures within the wheat kernel acted as an effective barrier to fungal invasion. Moreover, after inoculation by toxigenic Fusarium strains, semolina was shown to allow high yields of trichothecenes, while bran was demonstrated to contain biochemical inhibitors able to significantly reduce trichothecene production. These results will be useful in improving breeding strategies to control trichothecene contamination of durum wheat kernels.