Down syndrome (DS) is characterized by abnormal brain morphology and neurological and behavioral functions. The pivotal role of helicases in brain development, growth, and differentiation made us evaluate three DEAD BOX proteins, DEAD-box protein 1 (DBP-RB), DEAD-box protein 3 (HLP2), DEAD-box protein 72 (P72), and the RuvB-like DNA helicase (TIP49b), in fetal brain of controls and DS subjects, using two-dimensional electrophoresis with subsequent mass spectroscopic (MALDI-MS) identification. HLP2 and TIP49b brain levels were comparable between DS and controls, and protein levels of p72 and DBP-RB were significantly reduced in DS fetal cortex (p72: 2.04+/-1.90 vs. 5.57+/-2.56 in controls, p < 0.01; DBP-RB: 0.58+/-0.94 vs. 1.90+/-0.97 in controls, p < 0.01). Impairment of the helicases p72 and DBP-RB may reflect or lead to deficient growth and differentiation of brain development early in life and can be considered pathogenetic factors along with the reported deficits of transcription, splicing, and elongation factors already described in fetal DS brains.