The vast majority of angiosperms are (or were once) polyploid, and as hexaploid bread wheat has undergone two ploidy events separated by approximately 0.5 million years, it represents an elegant model to study gene silencing over time in polyploids. Using an SSCP platform, we have analysed patterns of transcriptional silencing (frequency, genome identity and organ specificity) within 236 single-copy genes, each mapping to one locus on one of the three homoeologous chromosomes within groups 1, 2, 3 and 7 of wheat. In about 27% of unigenes expressed in leaf, and about 26% of those in root, one (rarely two) members of a gene set (homoeoalleles) were not present in the cDNA template. Organ-specific regulation is commonplace, with many homoeoalleles transcribed in leaf but not root (and vice versa). There was little indication of extensive bias towards selective silencing of a particular genome copy. Expression of some of the silenced homoeoalleles was restored in certain aneuploid lines and varieties, and these displayed a significant degree of genetic variation for the silencing of a given homoeoallele. We propose that a substantial proportion of this phenomenon is effected by an epigenetic mechanism, and suggest that this form of genetic variation may be a significant player in the determination of phenotypic diversity in breeding populations.