To identify biomarkers associated with the development of hepatocellular carcinoma (HCC) in CuZn superoxide dismutase (CuZnSOD, Sod1) deficient mice, 2-DE followed by MS analysis was carried out with liver samples obtained from 18-month-old Sod1−/− and +/+ mice. The intra-cellular Ca binding protein, regucalcin (RGN), showed a divergent alteration in Sod1−/− samples. Whereas elevated RGN levels were observed in −/− samples with no obvious neoplastic changes, marked reduction in RGN was observed in −/− samples with fully developed HCC. GST mu1 (GSTM1), on the other hand, showed a significant increase only in the neoplastic regions obtained from Sod1−/− livers. No change in GSTM1 was observed in the surrounding normal tissues. Marked reduction was observed in two intracellular lipid transporters, fatty acid binding protein 1 (FABP1) and major urinary protein 11 and 8 (MUP 11&8), in Sod1−/− samples. Analysis of additional samples at 18−22 months of age showed a three-fold increase in enolase activities in Sod1−/− livers. Consistent with previous findings, carbonic anhydrase 3 (CAIII) levels were significantly reduced in Sod1−/− samples, and immunohistochemical analysis revealed that the reduction was not homogenous throughout the lobular structure in the liver.