The neuropeptide Y 5 receptor (NPY5R) plays an important role in the regulation of appetite and feeding behaviour in mammals by modulating the effect of the neurotransmitter neuropeptide Y. As single nucleotide polymorphism (SNP) variation in the bovine NPY5R gene is likely to influence the expression and/or function of this gene, the objectives of this study were to identify SNPs in the bovine NPY5R gene and to predict their functional role in the expression and physico-chemical characteristics of the protein product. Nineteen novel SNPs were identified in a 2.1 kb genomic region of the NPY5R gene in a total of 419 beef cattle from 13 Bos taurus breeds and eight Bos indicus animals. Four of these SNPs were non-synonymous (Met → Ile, Leu → Phe, Pro → Leu, Arg → Stop codon), while 10 were synonymous. Of particular interest was one non-synonymous SNP (c.1090C>T) that introduced a stop codon in the third intracellular loop of the NPY5R molecule. This stop codon is predicted to create a truncated NPY5R molecule with different physico-chemical properties compared to the native NPY5R protein. A further four SNPs were located in the 5' untranslated region (UTR) and one in the 3'UTR. Two of the 5'UTR SNPs affected putative transcription factor binding sites (GATA binding factor and snRNA-activating protein complex). In conclusion, regulatory and functional SNPs were identified in the bovine NPY5R gene. These include SNPs which potentially modify transcription factor binding sites as well as SNPs that cause amino acid changes and premature termination of the NPY5R protein. Such polymorphisms are likely to play vital physiological roles in the neuropeptide Y mediated appetite, feed intake and energy homeostasis in cattle.