Anther extrusion (AE) of wheat is a morphological trait that influences FHB resistance, particularly resistance to initial infection. In a one year field trial, 403 different breeding lines were evaluated for anther retention (AR) and FHB severity after spray inoculation with Fusarium culmorum. The wheat lines showed a significant variation for AE and FHB resistance and both traits were highly correlated (r = 0.50, P < 0.001). Selection for high AE, a highly heritable morphological trait, appears to be a promising strategy to enhance FHB resistance in breeding lines. In addition, the relationship between the major FHB resistance QTL Qfhs.ifa-5A and AR was analysed in more detail. Therefore, the susceptible cultivar ‘Remus and its near isogenic sister line ‘Remus-NIL3, carrying Qfhs.ifa-5A, were evaluated for both traits. ‘Remus exhibited higher degree of retained anthers and was more severely diseased than ‘Remus-NIL3. The association between AE and Qfhs.ifa-5A, which confers mainly resistance to initial infection, was further examined in a glasshouse experiment. Different pre-treatments, which were: (i) removing the anthers, (ii) compressing them inside the florets and (iii) control heads without pre-treatment, were applied to ‘Remus and ‘Remus-NIL3, prior to inoculation with the fungus. After single head spray inoculation, control heads of ‘Remus were significantly more diseased than ‘Remus-NIL3 control heads. When anthers were removed, ‘Remus and ‘Remus-NIL3 showed low disease severity and no significant difference in FHB severity was evident between the two genotypes. When the anthers were compressed inside the florets, ‘Remus was slightly more diseased than ‘Remus-NIL3. The results indicate that the major resistance QTL Qfhs.ifa-5A acts as a passive resistance mechanism controlling anther extrusion and FHB resistance.