Grain hardness is an important quality characteristic of wheat grain, and considerable research effort has focused on characterising the genetic and biochemical basis underlying the hardness phenotype. Previous research has shown that the predominant difference between hard and soft seeds is linked to the puroindoline (PIN) proteins. In this study the near-isogenic lines of Heron and Falcon, which differ only in the grain hardness character, were compared using a cDNA microarray consisting of approximately 5,000 unique cDNA clones that were isolated from wheat and barley endosperm tissue. Our analysis showed that major differences in gene expression were evident for puroindoline-a (Pina), with a minor but not consistent change in the expression of puroindoline-b (Pinb). These observations were confirmed using a 16,000 unique cDNA microarray in a comparison of hard wheats with either the Pina null or Pinb mutation.