The safety assessment for pharmaceuticals includes in vivo repeated dose toxicity tests in laboratory animals. These in vivo studies often generate false negative results and unexpected toxicity. The appearance of this unexpected toxicity is one of the major reasons for the drawback of a drug from the market. The liver is often a target organ in toxicology since it is responsible for the metabolism and elimination of chemical compounds. Therefore, there is need for new screening methods which classify hepatotoxic compounds earlier in development. This will lead to safer drugs and a more efficient drug discovery process. Furthermore, these new screening methods are preferably in vitro test systems, aiming at reducing the use of laboratory animals. In this review the possibilities of proteomics and its promising results for improving current predictive and mechanistic toxicological studies are described. Biomarkers or protein panels for hepatotoxic mechanisms, which reflect the in vivo situation, need to be identified to allow a better toxicity screening. Therefore, in vivo studies and in vitro cell models are discussed and evaluated with regard to the protein expression of their metabolic enzymes, their similarities with liver, their use for analyzing toxicological mechanisms and hepatotoxicity screening. Studies in which proteomics are combined with other omics-technologies are also presented. The results from these integrated data analyses can be used for the development of improved panels of biomarkers for toxicity screening.