CTCF has multiple function in epigenetics including X-chromosome inactivation, genomic imprinting and genome organization. Mutations in CTCF are known to cause intellectual disability, however mechanism underlying the disease remains unknown. In this study, we reported two patients with a deletion including CTCF and proposed CTCF deletion syndrome because they showed distinct clinical characteristics icluding intellectual disability. Surprisingly, X-chromosome inactivation and DNA methylation at imprinted loci were normal, while genome-wide DNA hypermethylation only at CTCF binding sites were demonstrated and two candidate genes, PRKCZ and FGFR2, were identified, suggesting the underlying mechanism of the syndrome. (By Drs. Ikumi Hori and Shinji Saitoh, http://jmg.bmj.com/content/early/2017/08/28/jmedgenet-2017-104854 )