Fusarium head blight (FHB) is a fungal disease which causes losses to farmers in many wheat production regions. The fungus induces shrivelling of the seeds directly affecting yield as well as losses in quality due to the production of mycotoxins. The contamination of the grains with mycotoxins is hazardous to humans as well as to animals. In the wheat gene pool large quantitative variation for resistance to Fusarium head blight is evident. In this study the association of the stem shortening genes Rht-B1 and Rht-D1 with resistance to Fusarium head blight was examined. Two double haploid populations derived from crosses between the parents HermanMulan and HermanNord010044 were artificially inoculated with Fusarium culmorum in a field experiment. The traits flowering date, plant height and FHB severity were visually assessed in both populations. The doubled haploid lines were examined at the molecular level using diagnostic PCR markers for genes Rht-B1 and Rht-D1. The dwarfing genes were not associated with flowering date in these populations. The lines which carried the 'semi-dwarf' alleles Rht-B1b or Rht-D1b both showed on average significantly reduced plant height (as expected), but also higher FHB severity than the plants with the 'tall' Rht-B1a or Rht-D1a alleles. However, there was large variation in FHB severity within each group for specific Rht-alleles. Therefore, the selection of moderately resistant wheat lines carrying one 'semi-dwarf' allele, either Rht-D1b or Rht-B1b appears feasible. On the other hand, selection of double-dwarf lines (Rht-B1b and Rht-D1b combined) with a good level of FHB resistance seems almost impossible.