Proximal region of chromosome 15 long arm contains a number of low copy repeats known as five breakpoints (BP: bp1, bp2, bp3, bp4 and bp5). As we know, the microdeletion, extending from BP1 to BP3 (type 1) or from imprinted region BP2 to BP3 (type 2), cause PradereWilli/Angelman syndrome, depending on the parental origin of the deleted allele. 15q11.2 microdeletion between BP1 and BP2 is characterized by is associated with mild dysmorphic features, developmental delay/intellectural disability, behavior problem, seizure/epilepsy and congenital heart disease. We describe a 3-year-old boy with a 15q11.2 BP1-BP2 microdeletion. His mother received genetic counseling on the increased nuchal translucency and underwent chorionic villus sampling. The prenatal karyotype analysis and multiple ligation probe amplification testing were performed. These results of analysis showed normal. He was born with complex congenital heart anomaly (coarctation of the aorta, atrial septal defect, and ventricular septal defect) and underwent heart surgery. His developmental milestones were significantly delayed. On physical examination, at the age of 3 years, he showed hypertelorism, downslanting palpebral fissures, strabismus, and short status. Base on the clinical features, the clinical diagnosis was Noonan syndrome. This 518 kb sized deletion on 15q11.2 identified using a 750K SNP Microarray (Affymetrix; Thermo Fisher Scientific, Inc., Waltham, MA, USA) at Green Cross Genome. This region contains four highly-conserved and non-imprinted genes: NIPA1, NIPA2, CYFIP1, TUBGCP5. Literature reviews indicated that the prevalence of a 15q11.2 BP1-BP2 microdeletion was suspected from 0.09 to 0.81%. To the best of our knowledge, this is the first report of genetically confirmed case in the Korean population. For diagnosis of patients with 15q11.2 BP1-BP2 microdeletion syndrome, chromosomal microarray analysis would be considered for pediatric patients with intellectual deficiency, behaviour issues and/or multiple congenital abnormalities.