Absence seizure has been of interest because the symptom is related to sensory processing. However, the mechanism that causes the disease is not understood yet. To better understand the molecular mechanism related to the disease progress at protein level, we performed proteomic studies using the thalamus of mice for which absence seizure was induced by gamma-butyrolactone (GBL). Differential proteome expression between GBL-treated mice and control mice was examined by fluorescence 2D difference gel electrophoresis (DIGE) at three different time points (5, 10, and 30 min) after GBL-administration. We identified 16 proteins differentially expressed by >1.4-fold at any of the three time points. All proteins besides the serine protease inhibitor EIA were down-regulated in absence seizure-induced mice. The down-regulated proteins can be classified into five groups by their biological functions: cytoskeleton rearrangement, neuroprotection, neurotransmitter secretion, calcium binding, and metabolism. The maximum level of change was reached by 10 min after GBL-treatment, with the expression level returning back to the original at 30 min when mice were awakened from absence seizure thereby demonstrating the proteomic response is reversible. Our results suggest that absence seizures are associated with restricted functional sets of proteins, whose down-regulation may interfere with general function of neuronal cells.