Copy number variation (CNV) is an important source of human genetic diversity, which contributes to Mendelian disorders as well as complex diseases. We conducted a genome-wide CNV discovery in 451 males of Han Chinese by using high-density comparative hybridization arrays. The CNVs we reported are in high quality and representative of Han Chinese from 28 dialects and diverse geographical regions. More than half of the variants are novel and have not been reported yet. These data are complementary to public sources of human genomic data, and the CNV map may facilitate in the identification of pathogenic CNVs and further biomedical studies involving the Han Chinese populations. (By Prof. Dr. Shuhua Xu, http://jmg.bmj.com/content/early/2017/07/13/jmedgenet-2017-104613 )