Biomarkers are viewed as an important tool in the rational drug development approach to candidate selection, attrition, optimization and confirmation; however, wide application of biomarkers in drug development has only become common practice in recent years. There are a series of issues relevant to biomarker terminology, including different systems of biomarker nomenclature, different uses of biomarkers, the range of types of biomarker assays from immunologic to expression profiling to imaging, and different strategies for validation (assay or method validation) and qualification (clinical validation) of biomarkers. An important distinction is between biomarker validation and qualification, where validation is the rocess of assessing the assay or measurement performance characteristics and qualification is evidentiary process of linking a biomarker with biology and clinical endpoints. There are a series of issues relevant to this distinction including differences between pharmacokinetic assay validation and biomarker validation, proposals for fit-for-purpose biomarker validation and qualification, and the interaction between validation and qualification. A dialogue on these issues is a major goal of more recent biomarker initiatives including those of AAPS and PhRMA.