CRISPR-Cas9 is a powerful tool with tremendous potential for the treatment of hereditary diseases. However, in addition to the well-described off-target genotoxicity, an on-target genotoxicity can occur when generating a targeted double strand break. This kind of genotoxicity induced by CRISPR-Cas9 nuclease is less known and needs to be further investigated. When targeting the globin genes, we discovered that genome editing could induces megabase-scale losses of heterozygosity from globin cut site to the telomere (5.2Mb). In HEK293T cells, CRISPR-Cas9 nuclease lead to the truncation of the terminal chromosome 11p region. In clinically relevant primary hematopoietic progenitor/stem cells, we detected clones with acquired megabase copy-neutral LOH induced by CRISPR-Cas9 leading to 11p15.5 partial paternal uniparental disomy. These clones presented imprinting defects and impaired transcriptional expression of genes located in the 11p15.5 region. This genotoxicity could be a safety concern for the development of gene therapy protocols but also an opportunity to model CN-LOH for genetic diseases and cancers.