Copy number variation (CNV) refers to genomic segments that present a type of structural variation, such as duplications or deletions. CNVs have been observed as an important source of genetic and phenotypic variation for production traits and animal health. The aim of this work was to identify CNVs in a synthetic breed (Gyr × Holstein) dairy cattle population (Girolando cattle). The data set contained 417 animals genotyped with the Illumina 50K SNP panel (~54.609 SNPs). An algorithm based on the Hidden Markov Model was implemented using PennCNV software (Wang et al., 2007) for CNV identification. PennCNV perl script was used to eliminate calls from low quality samples, based on the standard deviation of LRR (<0.30), the BAF drift (<0.01) and waviness factor (less than 0.05). The final data set was composed of 384 animals. Gene content of cattle CNV was assessed using Ensembl genes. We used the PANTHER classification system for testing the hypothesis (P < 0.05) that the GO terms of the molecular function, biological process, and pathway terms were under or overrepresented in the CNV. An account of 1,986 CNVs were found along the genome, of which 84% were duplications and 16% were deletions. The chromosomes BTA3, BTA17 and BTA23 presented higher frequencies (10.52%, 11.53%, 8.30%, respectively) of CNV. Chromosomes that showed lower frequency of CNV (<1%) were BTA27, BTA14 and BTA29. A total of 861 genes were found within these regions and they are involved in biological processes, such as development (105 genes), growth (2 genes), immune system (83 genes), metabolism (343 genes) and reproduction (12 genes). This study showed evidences of structural variations in the genome of Girolando cattle and the genes found in CNV may be involved in the expression of production and animal health traits.