The application of advanced modern biomedical and chemical research technologies in the pharmaceutical industry has led to a significant increase in the number of potential drug targets and lead candidates. Whereas the drug discovery process is enhanced significantly, the failure rate of new compounds due to toxicity remains very high. The pharmaceutical industry is setting high hopes on the new discipline of toxicogenomics to revolutionize the process of drug toxicity assessment by reducing the bottleneck of new drug candidates and minimizing late-stage developmental failures. Toxicogenomics is expected to facilitate the efficient screening of new compounds at an early stage, resulting in significant savings of time and cost associated with new drug development. In this review, a general description of the new discipline of toxicogenomics and its potential impact on the safety assessment of new drugs in the pharmaceutical industry is provided. An overview of the key issues and questions that are confronting investigators in this field today is also given as well as a prospective view of the future of this new discipline.