Objective Hes5 is one of the critical effectors of the Notch pathway and its expression can inhibit neuronal differentiation.Which protein expression is influenced in cell differentiation by Hes5 remains to be determined. Methods Experiments were designed to study changes in protein expression in the subventricular zone(SVZ) of the Hes5 knockout mice at the postnatal day 8 using the new method of proteomic isobaric tags for relative and absolute quantification （iTRAQ）, and confirmed expression of the up-gulated and down-regulated proteins by Western blotting. Results Nineteen proteins showed differences in expression levels in the SVZ of Hes5 knockout mice. When compared to the wild type mice, expressions of 11 proteins in the knockout mice were up-regulated, and the differentially expressed proteins showed ratios of knockout/widtype between 1.20 and 1.32. Expressions of 9 proteins were down-regulated, with their ratios were between 0.77 and 0.83. The up-regulated proteins have been shown to be involved in neurogenesis, cell adhesion, migration and signal transduction. The down-regulated proteins have been mainly shown to be involved in growth inhibition and cytoskeleton. Western blotting analysis further confirmed the expression of proteins from iTRAQ. Conclusion Our findings suggest that Hes5 may influence cell differentiation by regulating expression of some proteins involved in cell growth and migr