Trisomy 9 mosaicism syndrome is a rare chromosomal abnormality with a high incidence of natural abortion and perinatal death. This syndrome is characterized by intrauterine growth retardation, mental retardation, craniofacial dysmorphism including a prominent nasal bridge with a short root and a fish-shaped mouth with thin lips, skeletal abnormalities, congenital heart defects, and genital abnormalities. The incidence and severity of malformations depend on the percentage of trisomic cells in the different tissues. We report a neonate who had the characteristic features of trisomy 9 syndrome with dysmorphic features including micrognathia, microcephaly, a low-set and malformed ear, a prominent lip, and cardiac defect. No chromosomal abnormalities were detected on a routine peripheral blood chromosomal analysis; however, a chromosomal abnormality with trisomy 9 mosaicism (low-level mosaic type) was detected on genetic tests. This is thought to be due to the low proportion of trisomic cells, and for this reason, the patient in this case shows a better prognosis than four patients previously reported in Korea, they were all diagnosed by peripheral blood chromosome testing.