Irradiation induces a series of liver diseases. However the molecular mechanisms involving in the process of liver diseases induced by irradiation are still unclear. Subcellular proteomics provides a method to understand regional differences in protein expression levels. With accumulating evidence in the literature that new proteins are implicated in radiation response, in the present study, C57BL/6 mice were treated with irradiation, liver cell homogenates were subfractionated by differential ultracentrifugation into nuclei, mitochondria and cytosol, which were subjected to 2-DE to generate the proteomic maps of these fractions. The differentially expressed proteins in the nuclei, mitochondria and cytosol compartment of liver at 24 and 48 h after exposure to 20 Gy irradiation compared to control were identified by MALDI-TOF MS respectively. Total 37 proteins at 24 h and 29 proteins at 48 h were matched with known proteins after database searching in nuclei, mitochondria and cytosol, respectively, among which nine proteins exhibited changes at both time points. Most of these proteins are involved in antioxidant response, energy metabolism, molecular chaperones and inflammatory response. More antioxidant-associated proteins were induced at 48 h than 24 h. Reverse transcriptase polymerase chain reaction (RT-PCR) and Western blotting further validated 2-DE results of two of these proteins. It is feasible that the differential proteins identified in this study have a biological significance and may provided clues for understanding the mechanism of injury in liver induced by irradiation.