With the progress of molecular biology and other disciplines, biomarkers are becoming increasingly important in both drug discovery and development. Several critical issues, including scientific rationale, study design, marker assessment, cost and feasibility should be carefully considered in the validation of biomarkers through clinical research. Here, we highlight several important aspects related to the design for clinical researches which incorporate biomarkers. First, we define the term "biomarker" and illustrate the difference between prognostic and predictive markers. Second, in exploratory clinical studies, we focus on issues related to study design for screening and evaluating biomarkers. Finally, we review the design of confirmatory clinical trials for new treatments and companion biomarker diagnostic tests.