Using Affymetrix’s Chicken Genome Array, we used total RNA isolated from the gonads of male and female chicks at embryonic day 9 to identify the genes differentially expressed between male and female. Statistical results show 19 493 genes expressed in male chick’s embryonic gonads and 19 368 genes expressed in female. There were 145 genes specificity expressed in male and 189 genes in female. The gene ontology classification (GOC) indicated these differentially expressed genes were mainly involved in cellular component, cell process and molecular banding, a part of genes were involved in organelle component, metabolic process, biologic process, catalytic activity and signal transducer activity. Some genes had reported for sex determination and differentiation in birds, such as avian sex-specific avian sex-specific W-linked, chomodomain-helicase-DNA-binding protein 1 and sex determining region Y-box 9. In addition, we also found several genes or hypothetical proteins were unknown function for the gonad differentiation and development, focus to their biological function and expression pattern in further works would provide a beneficial reference for understand the mechanism of sex differentiation and determination in birds.