The ability and capacity to investigate bovine genetic variation is achievable now that the genome is sequenced, and massively parallel next-generation sequencing technologies take us one step closer to assessing the genetic variation between individual animals and diseases. However, considering the complexity, size, and repeat content of the bovine genome, there is an important need for new technologies that target and extract a defined subset of the genome for variation discovery. Historically polymerase chain reaction (PCR) has been the predominant procedure for the selection and enrichment of relevant genomic regions. However, PCR is labor intensive, expensive at large scale, and failure-prone. More recently, genotyping arrays have been used to assess genetic variation, however, to be effective they require prior knowledge about the location of genetic variants. To address these issues, we have developed a targeted genome capture strategy that specifically targets and isolates, in a parallel fashion, exons and regulatory regions of the bovine genome for resequencing and SNP discovery. The capture set contains probes designed against 222,000 regions, representing 46 million bases, of the bovine genome. Multiple Bovine HapMap DNA samples from the USDA-ARS-BFGL, were captured and sequenced on the Illumina GAIIx and HiSeq 2000 platforms. We will present results that analyze and assess the technical performance of the Bovine capture set with respect to depth and breadth of coverage of targeted areas and hybridization specificity. In addition, we will characterize the percentage of concordant SNP calls, compared to HapMap, for each individual animal.