Biomarkers are characteristics objectively measured and evaluated as indicators of: normal biologic processes, pathogenic processes, or pharmacologic response(s) to a therapeutic intervention. In environmental research and risk assessment, biomarkers are frequently referred to as indicators of human or environmental hazards. Discovering and implementing new biomarkers for toxicity caused by exposure to a chemical either from a therapeutic intervention or accidentally through the environment continues to be pursued through the use of animal models to predict potential human effects, from human studies (clinical or epidemiologic) or biobanked human samples, or the combination of all such approaches. The key to discovering or inferring biomarkers through computational means involves the identification or prediction of the molecular target(s) of the chemical(s) and the association of these targets with perturbed biological pathways. Two examples are given in this chapter: (1) inferring potential human biomarkers from animal toxicogenomics data, and (2) the identification of protein targets through computational means and associating these in one example with potential drug interactions and in another case with increasing the risk of developing certain human diseases.