Objective To compare the gene expression profiles of fore and hind limbs in mice and screen out genes specifically expressed in hind limbs. Methods Mouse fore and hind limb gene expression chip data were obtained from the NCBI GEO database. The raw data (five forelimb E10. 5 day chips and four hind limb E10. 5 day chips) were quality-controlled using the Transcriptome Analysis Console software. The data were filtered to identify differentially expressed genes (DEGs) using the criteria: difference > 2 times or < 0. 5 times and P-value. We drew volcano maps and performed cluster analysis with the DEGs. A gene interaction network map was constructed with the hind limb-specific genes. Results There were 275 DEGs in the hind limbs of mouse E10. 5 embryos, of which 45 genes were upregulated and 230 genes were downregulated. The hind limb-specific DEGs were mapped to the gene network and the core node genes of hind limbs were identified. qPCR was used to investigate some of the hind limb-specific genes, and the results were consistent with the chip results. Conclusions Mouse expression microarrays are successfully used to screen the genes specifically expressed in hind limbs, which provide a basis for the study of mammalian limb development.