The polymerase chain reaction (PCR) is a relatively new molecular biology-based technique that allows the specific identification of small amounts of DNA or RNA. This technique offers significant advantages compared to conventional microbiological tests, such as microscopy or culture. Increasing numbers of immunosuppressed patients with intraocular infections and, improvements in antibiotic therapy for specific organisms require a more accurate diagnosis. PCR is capable of providing such requirements. This technique is evolving rapidly and in cooperation with clinicians and molecular biologists a number of applications are being developed, which contribute to the growing demands on microbiological testings. This article describes the basics, indications and the limitations of the polymerase chain reaction.