The storage proteins of wheat (Triticum aestivum L.) form large polymers commonly referred to as gluten. These polymers are critical in determining important traits, especially in the processing qualities of dough. Vast amounts of research on the storage proteins and the genes encoding them have revealed the impact of different alleles on the properties of wheat dough. However, little is known about factors that may play a role in the folding, association and deposition of the storage proteins. One such factor could conceivably be the enzymes involved in catalysing folding of nascent proteins appropriately, the ‘foldase’ enzymes, including members of the protein disulfide isomerase (PDI) and cyclophilin families. Little is known about the genes encoding these enzymes in wheat, this information being limited to expression data showing the up-regulation of these genes in the developing endosperm, cDNA clones previously isolated in our lab and a report of partial PDI genes. One strategy to determine an association of the genes with important traits is to develop molecular markers and identify any genetic linkage between these gene-specific markers and quantitative trait loci related to dough quality. Thus, this project involved the characterisation of the gene families encoding PDI and cyclophilin in wheat and assessment of these genes for intercultivar polymorphism that could be used to develop ‘perfect’ molecular markers for these genes. Further, orthology between the PDI loci in wheat and the esp2 locus in rice, which has been associated with irregular storage protein deposition, is described.