Abstract: Peptidomics is an extension of proteomics. The target of peptidomicsis endogenous peptides with molecular weight less than 10 ku in organs, tissues, cells and body fluids. Body fluid peptides contain abundant pathological and physiological information of human. The studies of body fluid peptides as biomarkers had attracted tremendous attentions since they were proposed in 2000. This review covered the research methods of peptidomics and the development and application of three kinds of body fluid peptidome biomarkers, which pointed out the versatility of peptidomics. The disadvantages of using peptide molecular weight as biomarkers were also discussed. It indicated that some uncertainty might be introduced in each step of peptide analysis.