Neuro-degeneration early in fetal development in the brains of Down syndrome (DS) patients is proposed to result in the apparent neuropathological abnormalities, and to contribute to the phenotypic character such as mental retardation and premature development of the pathologies of Alzheimer disease, those being the most common phenotype in DS. In order to dissect and identify the aberrant and specific genes manifested as developmentally associated in the early differentiating DS neurons, we have utilized an in vitro neuronal differentiation system of mouse ES cells containing a single human chromosome 21 [TT2F/hChr21] as a model of DS neuronal development, with TT2F parental ES cells as a control. This TT2F/hChr21 cells is observed higher apoptosis phenotype than normal controls in the early differentiation of neuronal stem cells.The paired protein extracts from TT2F and TT2F/hChr21 cells at several stages of neuronal differentiation were subjected to 2-DE protein separation followed by MALDI-TOF-MS to identify the proteins differentially expressed between TT2F and TT2F/hChr21 cells. We provide here a novel set of specific gene products altered in early differentiating DS neuronal cells, which is different from that identified in adult or fetal brain with DS. The aberrant protein expression in early differentiating neurons, due to the hChr21 gene dosage effects or chromosomal imbalance, may affect the neuronal outgrowth, proliferation and differentiation implying the developmental abnormalities in neural patterning eventually leading to formation of a suboptimal functioning neuronal network in early life.