Polymerase chain reaction (PCR) techniques comprise some of the most powerful tools in molecular biology research. PCR is characterized primarily by the ability of polymerases to amplify specified regions of DNA both rapidly and efficiently and overcomes the lengthy procedures usually associated with in vivo DNA cloning methods. Discovery and development of the PCR technique into a viable and powerful research tool occurred in the mid-1980s (1). Numerous publications give testament to the robust nature of this technique and to its flexibility, evidenced by its application in diverse experimental situations and the ever increasing range of PCR-based techniques. Many complete books are dedicated to PCR technologies and cover a broad range of aspects that are beyond the scope of this chapter (see, for example, 2–5, which we have found useful). Our goal instead is to outline some basic PCR-based techniques commonly used in the identification of neuropeptide-encoding DNA and to highlight the major problems typically encountered.