Objective To explore the molecular mechanism of hypophrenia induced by Down syndrome (DS).Methods Ts65Dn mice were used as DS animal model.Three female mice and three male mice of three to twelve weeks old were mated.Among the 17 first-generation mice alive,five mice remained Ts65Dn trisomy and 12 mice were normal.Five Ts65Dn mice and five normal mice were selected randomly as Ts65Dn group and control group,and bred till 16 to 18 weeks old for experiments.Differential proteins in hippocampus of mice were tested by isobaric tags for relative and absolute quantitation (iTRAQ).Expressions of the differential proteins in Ts65Dn group were detected compared with those in control group.Results A total of 2805 proteins were identified in hippocampus of Ts65Dn group and control group,and significant differences were observed in the expressions of 374 proteins.Compared with those in control group,expressions of 195 proteins increased and 179 reduced in Ts65Dn group.Sorted by P value from low to high,the seven proteins with the lowest P value were uncharacterized protein C2orf47 homolog,isoform 2 of filamin A-interacting protein 1-like,zinc finger protein,isoform 1 of pericentriolar material 1 protein,SEC23 interacting protein,BAG family molecular chaperone regulator 3 and serpin H1.Conclusions Differential proteins are observed in hippocampus of Ts65Dn mice,perhaps closely correlating to neurological defects.The new technology of iTRAQ helps to screen and identify differential proteins in hippocampus.