Copy number variations (CNVs) are important large-scale variants. They are widespread in the genome and maycontribute to phenotypic variation. Detection and characterization of CNVs can provide new insights into the genetic basis ofimportant traits. Here, we perform whole-genome short read sequence analysis to identify CNVs in two indigenous and com-mercial chicken breeds to evaluate the impact of the identified CNVs on breed-specific traits. After filtration, a total of 12 955 CNVsspanning (on average) about 9.42% of the chicken genome were found that made up 5467 CNV regions (CNVRs). Chickenquantitative trait loci (QTL) datasets and Ensembl gene annotations were used as resources for the estimation of potentialphenotypic effects of our CNVRs on breed-specific traits. In total, 34% of our detected CNVRs were also detected in earlier CNVstudies. These CNVRs partly overlap several previously reported QTL and gene ontology terms associated with some importanttraits, including shank length QTL in Creeper-specific CNVRs and body weight and egg production characteristics, as well asmuscle and body organ growth, in the Arian commercial breed. Our findings provide new insights into the genomic structure ofthe chicken genome for an improved understanding of the potential roles of CNVRs in differentiating between breeds or lines.