The absence of expression of individual members of a homoeologous set of genes in a polyploid is a well-established phenomenon. However, the extent to which such 'homoeologous silencing' can vary between individual genotypes within a species is unexplored. We have used the single-strand conformation polymorphism assay to identify homoeologue non-expression at 15 single-copy genes across a panel of 16 wheat varieties, representative of the genetic diversity present in modern northern European winter wheat (Triticum aestivum). There was no evidence for any homoeologous silencing at seven of the fifteen genes, but in the remaining eight, at least one of the three homoeologues varied qualitatively for expression in either the root or the seedling leaf. The identity of the non-expressed homoeologue was generally consistent, but when the expression profiles of eight informative genes were compared, only two varieties shared the same pattern of silencing. A small-scale study suggested that silencing patterns were largely inherited across self-pollinated generations, and some evidence is presented for the epigenetic segregation of these patterns in a population bred from parents having contrasting silencing profiles. Epigenetic variation exerts a significant effect on phenotype, so given the ubiquity and variability in homoeologous silencing observed in wheat, we suggest that it is likely to play a considerable role in generating phenotypic variation. Thus epigenetic profiling may need to be incorporated as part of the analytical tool kit for predictive wheat breeding.