We present a cytogenetically normal neonate who developed transient abnormal myelopoiesis. The blasts showed trisomy 21. In contrast, fibroblasts, and PHA-stimulated peripheral blood demonstrated normal diploid line on extensive karyotyping. Direct sequencing of the DNA derived from the peripheral blood at overt disease revealed splice site mutation in the boundary of GATA1 exon 2. The patient received three courses of chemotherapy leading to complete remission. During the complete remission, there was neither mutation of GATA1 exon 2 nor trisomy 21, confirming somatic nature of both abnormalities. The patient is now free from the disease 12 months after remission. This case emphasizes the significance of trisomy 21 as the cause of transient abnormal myelopoiesis in Down syndrome.