OBJECTIVE To present prenatal diagnosis and molecular genetic analyses of mosaic trisomy 9. RESULTS A 35-year-old woman, gravida 3, para 1, underwent amniocentesis at 17 weeks of gestation because of her advanced maternal age. Amniocentesis revealed a karyotype of 47,XX,+9[3]/46,XX[6]. Repeat amniocentesis at 19 weeks of gestation revealed a karyotype of 47,XX,+9[6]/46,XX[19]. At 22 weeks of gestation, she was referred to a tertiary medical center for genetic counseling, and amniocentesis revealed a karyotype of 47,XX,+9[2]/46,XX[22]. Array comparative genomic hybridization analysis of uncultured amniocytes revealed no genomic imbalance in chromosome 9. However, interphase fluorescence in situ hybridization analysis of uncultured amniocytes showed that nine (18%) of 50 cells were trisomic for chromosome 9. Polymorphic DNA marker analyses also revealed a diallelic pattern with unequal biparental inheritance of chromosome 9 and a dosage ratio of 1:18 (paternal allele:maternal allele) in the uncultured amniocytes and a dosage ratio of 1:36 in the cultured amniocytes, indicating that the euploid cell line had maternal uniparental isodisomy for chromosome 9. Level II ultrasound demonstrated bilateral ventriculomegaly. The pregnancy was subsequently terminated, and a malformed fetus was delivered. Postnatal cytogenetic and polymorphic DNA marker analyses of the fetal and extraembryonic tissues confirmed the prenatal diagnosis. CONCLUSIONS Mosaic trisomy 9 carries a high risk of fetal abnormalities warranting detailed sonographic investigation of congenital malformations. Mosaic trisomy 9 can be associated with maternal uniparental disomy for chromosome 9 in euploid cell lines. Array comparative genomic hybridization is limited for the detection of low-level mosaicism.