Objective: To detect and analyze a supernumerary derivative chromosome 15 with combined cytogenetic and molecular techniques, and to discuss the correlation between genomic copy number variations (CNVs) and clinical phenotypes. Methods: G-banded chromosome analysis and multiplex ligation-dependent probe amplification (MLPA) were carried out. The whole genome of the patient was also analyzed with array-comparative genome hybridization(array-CGH). Results: G-banding analysis indicated that the patient has a karyotype of 47,XY, + mar, with the supernumerary chromsome derived from 15qll13 region spanning 9.8 Mb from locus 20477397 to 30298155. Conclusion: CNVs of 15q11-13 are associated with mental retardation, language development delay and autistic disorder. Conventional cytogenetic analysis with array-CGH may provide a platform for accurate detection of chromosomal aberrations, which can faciliate the study of genome rearrangement underlying various diseases.