Abstract-Amelogenin (AMEL) is a conserved gene located on the sex chromosomes of mammals. It is involved in the formation of enamel, which is the hard, white material that forms the protective outer layer of each tooth. In this study, we first cloned the coding sequences of the goat AMELX and AMELY transcripts from female and male lamb enamel tissues during tooth development. All 207 amino acids of the putative AMEL proteins from the cDNA coding regions of both sex chromosomes were the same, but the AMEL sequences of the 3'-untranslated regions (UTR) were different. The results showed that the nucleotide sequences of intron 5 of the goat AMELX and AMELY genes contained multiple deletions/insertions and had only 48.5% identity. Based on the dimorphic AMEL intron sequences, a set of sex-specific primers was successfully applied to goat gender determination. A high sensitivity for sex determination was reached with a minimal amount of template, such as a trace amount of genomic DNA from a single blastomere isolated from embryos at the blastula stage among different strains of goats.