Neuropeptide Y (NPY) is one of the most potent orexigenic factors that is implicated in the control of feeding behavior and energy homeostasis. Four Chinese indigenous cattle breeds (n=338) were used to detect single nucleotide polymorphisms (SNPs) in the coding regions with their intron-exon boundaries and the proximal flanking regions of NPY gene by PCR-SSCP and DNA sequencing. Five novel SNPs (38017 C>G, 34240 C>A, 34168 G>A, 32463 A>C and 32302 C>G) were identified. Polymorphisms of P3 lous in NPY gene, containing SNP4 and SNP5, were associated with body length and chest girth in Nanyang cattle aged 6, 12 and 18 months (P<0.05), but they had no significant effect on the two growth traits in Nanyang cattle aged 24 months (P>0.05). The results open a new field of study and extend the spectrum of genetic variation of the bovine NPY gene, which might contribute to cattle genetic resources and breeding.