An investigation into the effect of microwaves on the fungal pathogens of winter wheat was undertaken. This was achieved by microwaving seed at 0, 15, 30 and 45 s. Agar plate tests and DNA analysis were then used to assess pathogen loads and germination, emergence and tetrazolium tests used to investigate seed viability after treatment. Throughout all treatment times, microwaving significantly reduced levels of contamination on seed and was particularly effective at controlling Fusarium spp. and Microdochium nivale. Conventional seed survived microwave treatment better than organic seed. Subsequent analysis and experimentation revealed that seed moisture content was inherently linked to losses in seed vigour upon exposure to microwaves. Seed levels of fungal DNA did not decrease with the observed loss of culturable fungal propagules, thus fungal death was attributed to heat and desiccation rather than denaturing DNA. Microwave treatment of wheat seed may offer a method to significantly reduce fungal loads on both conventional and organic wheat seed. Crown Copyright 2013 Published by Elsevier Ltd. All rights reserved.