Duplication 9p syndrome (partial trisomy 9p) is characterized by craniofacial anomalies, mental retardation, and distal phalangeal hypoplasia. Here, we present a female patient with microcephaly and incomplete bilateral cleft lip and palate, whose initial cytogenetic analysis revealed a de novo trisomy 9p. The patient, now 21 years old, has persistent microcephaly, craniofacial and hand anomalies, history of a seizure disorder, and global mental retardation. Oligonucleotide-based array comparative genomic hybridization was performed and revealed partial trisomy 9p21.1->9pter and a deletion of 9p12.1 to 9p11.2. Our case supports the utility of array comparative genomic hybridization for the precise characterization of chromosomal anomalies and for the ascertainment of genotype-phenotype correlation in patients with partial trisomy 9p.