Atrazine (ATZ), the most common herbicide, is a frequently observed contaminant in freshwater ecosystems. In the present study, two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization tandem time-of-flight-mass spectrometry, combined with histopathological analysis, were used to detect the hepatic damage in adult female zebrafish (Danio rerio) exposed to ATZ. More than 600 hepatic protein spots were detected in each gel with silver staining, and most of the proteins ranged from 20 to 70 kD and pH 4-9. Through comparison and analysis, 7 proteins were found to be upregulated>2-fold, whereas 6 protein spots were downregulated>2-fold after 10 and 1000 μg/l ATZ exposures for 14 days, which had caused histological effects in zebrafish livers. We found that these changed proteins were associated with a variety of cellular biological processes, such as response to oxidative stress, oncogenesis, etc. The results demonstrated that ATZ comprehensively influenced a variety of cellular and biological processes in zebrafish. The information presented in this study will be helpful in fully understanding the mechanism of the potential effects induced by ATZ in fish.