Despite huge investments, there are still difficulties in the development of novel therapies. This has led to a growing interest in the use of new tools, such as biomarkers, that can help overcome development hurdles while providing increased certainty about drug safety and efficacy. Until recently, no formal process has existed for qualifying biomarkers for regulatory decision making. The FDA's Center for Drug Evaluation and Research (CDER) has initiated such a process, which has led to the recent qualification of two biomarker sets for use in regulatory decisions. This article provides the reader with an overview of the CDER Biomarker Qualification Process and is shaped by the recent regulatory developments in biomarker qualification and the consideration of frequently asked questions in the area. The Biomarker Qualification Process is intended to be a mission-critical, value-added CDER program. The success of this effort will depend on the willingness of pharmaceutical and diagnostic companies, consortia, the FDA and other regulatory agencies to continue to work together, motivated by the benefits that can accrue to public health through the increasing availability of qualified biomarkers for use in drug development.