While this book’s theme is proteomicsproteomics and virology, this chapter on the role of proteomics in clinical virologyclinical virology may seem unsatisfying to the reader. The reason is simple: proteomics has not made a major impact on the diagnosing of viral infections. However, it is still important to evaluate the present role of proteomics in clinical virology as it provides a vision of what is required if it is to ever have a major impact in diagnosing viral infections. This chapter will initially provide a background on current techniques for diagnosing viral infections. Although the names may not be familiar to the casual reader, the techniques will be as most individuals have been tested using one of these techniques during their lifetime. The chapter will later switch to describe proteomic methods for the direct detection of viruses in clinical samples. While outside the scope of this book, a proteomic method for bacterial identification is included because (i) it describes a proteomic technology that has been approved by the FDAFDA for clinical use and (ii) since viruses and bacteria are both infectious agents it demonstrates the potential of proteomics for overall pathogen detection. To keep the topic in perspective, however, the advantages and disadvantages of using proteomics in clinical virology are compared to current existing methods particularly those that target the detection of genomic features within these pathogens.