KBG syndrome is a rare autosomal dominant congenital syndrome comprising developmental delay with various neurological involvements, macrodontia of the upper central incisors, characteristic facial dysmorphism, and skeletal anomalies. ANKRD11 was recently identified as the gene responsible for this syndrome. To date, there have been only five KBG syndrome families described, each carrying a single base substitution or a 1- to 14-bp deletion of this gene. Here, we present a patient with clinically confirmed KBG syndrome carrying a de novo 690-kb deletion at 16q24.3 involving part of ANKRD11. He had characteristic facial appearance, macrodontia of the upper central incisors, hand anomalies, delayed bone age and intellectual impairment without autistic features. Interestingly, the deleted region overlaps with the critical region for 16q24.3 microdeletion syndrome. We discuss the clinical entities of KBG syndrome and 16q24.3 microdeletion syndrome from a clinical and genetic point of view. © 2013 Wiley Periodicals, Inc.