In the present study, a brain and spinal cord cDNA library of Gekko japonicus was constructed, and 2349 unique expressed sequence tags (ESTs), composed of 494 clusters and 1855 singletons, were determined from 4108 randomly selected clones. Of these sequences, 54.8% (1287/2349) ESTs are identified as known genes and 45.2% (1062/2349), as unknown genes. The identified ESTs were classified with respect to their functional categorization; both the housekeeping genes and the nervous system-related genes were well represented in the library. The complete open reading frame (ORF)-containing clones derived from the library were identified as well; 303 clones were obtained to date. Finally, two clones with sequence homology to endothelial differentiation-related factor 1 (EDF-1) and to myelin-associated glycoprotein (MAG) precursor were selected, and their expression patterns in normal and regenerating spinal cord were analyzed by RT-PCR. Both of them were expressed in the spinal cord, and the expression level decreased significantly after tail amputation. This study provides a preliminary view of the gene expression profiles of the central nervous system in gecko, and it might accelerate the process of gene discovery and function analysis in this organism, which demonstrates an intrinsic capacity of spinal cord regeneration.