Previous studies have shown that heterosis is associated with differential gene expression between hybrids and their parents. In this study, we performed a screen for genes that are differentially expressed between wheat hybrids and their parents in jointing-stage leaves and flag leaves using the differential display technique. Twenty-four differentially expressed cDNA were cloned and sequenced, and their expression patterns were confirmed by reverse-Northern blotting. Sequence analysis and database searches revealed that among the genes that showed differential expression between hybrid and parents were transcription factor genes and genes involved in metabolism, signal transduction, disease resistance, and retrotransposons. These results indicate that hybridization between two parental lines can cause changes in the expression of a variety of genes, and it is concluded that the altered pattern of gene expression in the hybrid may be responsible for the observed heterosis.