Microdeletion of 9q22.3 is a rare chromosomal disorder characterized by body overgrowth, facial dysmorphic features and psychomotor delay. The presence of genomic microdeletion or microdu-plication can not be identified by the conventional chromosomal analysis. Microarray comparative genomic hybridization (CGH) is a newly developed molecular cytogenetic technique that enables the identification of minute copy number variation (CNV) in the human genome. Here, we report a case of microdeletion in the 9q22.31-q22.33 region, which included a patched homolog 1 (PTCH1) gene, as detected by CGH and confirmed by fluorescence in situ hybridization (FISH) analyses in a neonate with prenatal onset of macrosomia, dysmorphism, and muscle hypotonia. To the best of our knowledge, this is the first case report of 9q22.3 microdeletion detected by CGH in Korea.