Biomarkers may be applied to the understanding of the mechanism of disease, early diagnosis, prediction of the effect of the therapy and finding new drugs. Although the applications of biomarkers are useful, only few biomarkers are found and used in the clinical area. Besides, most clinically established markers (e.g. prostate specific antigen (PSA) for prostate cancer, cancer antigen CA125 for ovarian cancer) are lack of sensitivity and specificity. Therefore, the discovery of new biomarkers is a hot area. Due to the proteomics research has the potential of identification of biomarkers, it becomes a focus of the clinical research. This paper reviews the progress of biomarker discovery in the clinical research through proteomics.