Peptide biomarkers may be derived from nature or generated synthetically for a wide range of biomedical and medicinal chemistry applications. Naturally occurring peptides have taken on a variety of roles in molecular cell biology, including immune surveillance, metabolism, cell signalling and differentiation. Native peptides such as hormones, cell-penetrating peptides and immunostimulatory peptides have been implicated in regulating important biological functions and some have been administered for therapeutic treatment. Peptide biomarkers have been selected through in vitro phage display biopanning, synthetic combinatorial chemistry and bio-analytical peptidomic profiling techniques that have led to the discovery of important structure–function properties of biological markers in cells. Moreover, the development of new and more powerful analytical techniques such as genomic and proteomic analyses have led to the discovery of new biomarkers from cell culture, tissue samples and human biopsies. These studies have led to important findings in molecular cell biology which have facilitated the utility of lead peptide biomarkers in the detection and treatment of human diseases. In this chapter, a brief overview of selected peptide biomarkers is be discussed in the context of their natural design, synthetic development and applications in disease diagnosis and treatment.