We document a 2-year-old boy with developmental delay, mild mental retardation, and severe craniofacial malformation, including facial asymmetry with hypoplasia of the left zygoma, maxilla, and mandible, and left anophthalmia and anotia.G-banding (~550 band level) showed a normal 46, XY karyotype.A genome-wide screen for copy number variations (CNVs) using single nucleotide polymorphism (SNP) arrays revealed a 1.38Mb duplication on chromosome 1q31.1, which was absent in the parents and in 26 controls.