Copy number variants (CNV) represent a large proportion of genetic variation within the cattle genome that has yet to be accurately characterized by SNP genotyping arrays. While significant progress has been made in the identification of CNVs within individual animals using next generation sequence data, CNV frequencies within larger populations have not yet been estimated in cattle. In this study, we sequenced 28 individual bulls from 2 dairy breeds of cattle (22 Holstein bulls; 6 Jersey bulls) to identify dairy breed-specific copy number variation. Using a read depth method of CNV detection, we identified 1359 non-redundant CNV regions within all 28 animals. The number of variable bases contained within these CNV regions accounts for ~2% of the cattle genome, and the average CNV region frequency was 37.67%. This high average frequency suggests that a large proportion of CNVs were present in the ancestral population of both breeds of cattle rather than as a result of a large number of de novo events arising in subsequent generations after breed formation. We also assigned copy number values to each gene within each individual sequenced using the normalized sequencing read depth of non-overlapping genomic windows. Using a Vst approach on these gene copy number values, we identified 27 gene families with breed specific copy number expansions/contractions. We identified a Jersey-exclusive expansion of the CLEC5A gene, which is a regulator of osteoclastogenesis. Additionally, we identified a Holstein-exclusive duplication of the ASAP1 gene, which may be involved in cell membrane trafficking and the differentiation of fibroblasts into adipocytes. CNVs identified by this survey intersected gene families that may play a role in productive traits in dairy cattle and are therefore good candidates for novel genetic marker design.