Copy number variants (CNVs) are an important source of genetic variation, responsible for both Mendelian disorders and other positive attributes such as adaptive fitness. Knowledge of the location and distribution of CNVs in a genome is therefore very important. The aim of this study was to determine the distribution of CNVs in the goat genome in 13 East African goat breeds from Ethiopia, Kenya, Uganda and Tanzania. This study used genotype data based on a 52K single nucleotide polymorphism (SNP) chip from 433 animals. CNVs were detected using a hidden Markov model implemented in PennCNV software. A total of 946 CNVs were detected in 380 animals (613 copy losses and 333 copy gains). The CNVs spanned 325 CNV regions (CNVRs) of which 42 were found in 2 or more breeds with a frequency of more than 1%. Majority of these 42 CNVRs (29) were copy losses, 10 were copy gains and 3 were both. Notable CNVRs were copy gains on chromosomes 17 (59.9-61.2 Mb) and 24 (59.1-59.7 Mb) with a frequency of 34% and 11%, respectively, and occurring in all the 13 breeds and 4 breeds, respectively. This study has provided the first steps towards building a CNV map for the goat genome.