Peptide aptamers are combinatorial protein molecules with specific bind affinity to given target proteins under intracellular conditions. The typical structure of peptide aptamers is a short peptide region inserted within a scaffold protein. The short peptide region is responsible for binding with its target protein and the scaffold protein helps to enhance the binding affinity and specificity through restriction on the conformation of the binding peptide. This unique structural feature allows peptide aptamers to bind with their target proteins with strong affinity and high specificity. Applications of peptide aptamers thus vary from in vitro detection of various proteins in a complex mixture to in vivo modulation on proteins and cell functions. Peptide aptamers have also been considered as therapeutic molecules because of their anticancer and antivirus activity. Due to the importance of peptide aptamers, a general review on the structure, selection and applications of peptide aptamers in biological study as well as in therapeutics will be presented in this paper.