The field of biomarker discovery has exhibited a great surge of interest in recent years. Biomarkers can be used for many purposes including diagnosis, prognosis and selecting appropriate patient therapy, and can provide information on disease mechanism or progression. Translation of such markers to clinical testing encompasses phases for their discovery and characterization, assay development, and finally, implementation using automated platforms employed in clinical laboratories. With a focus on protein-based biomarkers and clinical immunoassays, the three phases are discussed in greater detail. The currently used technologies in the clinical laboratory are described, including attributes of existing immunoassay types, and some recent advances in methods development for multiplexed immunoassays. Finally, regulatory considerations that need to be addressed before a biomarker assay is commercialized are discussed briefly.