Abstract: The objectives of the present study were to elucidate the polymorphism of ovine neuropeptide Y (NPY) gene and its relationship with litter size of Small Tail Han sheep, and to provide a scientific basis for markerassisted selection for prolificacy in sheep. The NPY gene was studied as a candidate gene for prolificacy in some sheep breeds. Single nucleotide polymorphisms (SNPs) of all three exons (exon 1, 2 and 3) of NPY gene were detected in Small Tail Han, Hu, Texel and Dorset sheep by polymerase chain reactionsingle strand conformation polymorphism. Only the product amplified by primer P1 displayed polymorphism. Five genotypes were detected in Small Tail Han sheep, three genotypes in Hu and Dorset sheep, but only one genotype in Texel sheep. Sequencing results revealed that there were three alleles (CR, TR and TW) in Small Tail Han sheep, two alleles (CR and TR) in Hu and Dorset sheep, only one allele (CR) in Texel sheep. Compared with CR allele, there was one single nucleotide mutation (C→T) at 93 bp position of coding region of NPY gene in the TR allele. Compared with CR allele, besides C93T mutation, there was one double nucleotide mutation (GA→AT) at 130 and 131 bp position of coding region of NPY gene in the TW allele. This mutation caused an Asp→Ile replacement at position 16 of amino acid sequence of sheep NPY mature peptide. For C/T polymorphic site, the differences of the litter size between three genotypes were nonsignificant in Small Tail Han sheep (P>0.05). For GA/AT polymorphic site, the ewes with genotype RW had 0.56 (P<0.05) lambs more than those with genotype RR in Small Tail Han sheep. In the five combined genotypes of Small Tail Han sheep, the difference of the litter size between TTRW and CTRW genotypes was nonsignificant (P>0.05), the differences of the litter size between TTRR, CTRR and CCRR genotypes were nonsignificant (P>0.05), least squares means of litter size for TTRW and CTRW genotypes were significantly higher than those for the other genotypes (P<0.05). These results preliminarily indicated that allele W of GA/AT polymorphic site of NPY gene is a potential DNA marker for improving litter size in sheep.