mRNA differential display was used to analyse differences of gene expression between cross combinations, EC and CE, and their parental inbreeds, White Plymouth Rock (EE) and Silkies (CC). Three genes specifically expressed and one gene over-expressed in hybrids were found. By cloning, sequencing and BLAST analysis, one specific expression cDNA band was identified as the cytosolic isocitrate dehydrogenase gene, two were new genes of unknown function, and the over-expressed one was a proteosome subunit p112 gene. The results imply that functional and regulatory genes, expressed or over-expressed in chicken hybrids, are related to heterosis of some carcass traits.