The polymerase chain reaction is a powerful molecular biologic tool that allows the rapid production of analytic quantities of DNA from small amounts of starting material. Since the introduction of its modern form in 1988, PCR has revolutionized much of molecular biology and has greatly accelerated the development of molecular diagnostics. Kary B Mullis from USA received a Nobel Prize in 1993 for inventing this technique. This powerful technique has numerous applications in diagnostic pathology, especially in the fields of microbiology and genetics. All practicing ophthalmologists should have a working knowledge of the uses of PCR. PCR has been used to diagnose uveitis, infectious endophthalmitis and protozoa eye diseases. In this chapter we discusses the use of PCR in the analysis of uveitis, and ways in which PCR is improving our knowledge of understanding of the mechanisms of uveitis. Polymerase chain reaction is a powerful molecular technique for evaluation of very small amounts of DNA and RNA. PCR can be a simple, rapid, sensitive and specific tool for the diagnosis of infection, autoimmunity and Masquerade syndromes of the eye.