Recent advances in the basic understanding of both human biology and animal models have enabled an unprecedented level of information to be gathered about the genetic regulation of human disease. However, a corresponding insight into functional interactions between genetic information and protein expression has been slower to accumulate. Measuring mRNA transcripts does not yield a complete set of information about the protein dynamics involved in tissue injury and repair. Proteomics methods applied to unravel these relationships rely upon the identification and analysis of the proteins present within selected tissues and cells. Our understanding of complex biological processes can be enhanced by exploring the differences in protein structure and function between normal and injured tissues. This review concentrates on the development and application of proteomics techniques to uncover the specific processes and pathways involved in tendon injury and chronic tendinopathy.