Standard polymerase chain reaction (PCR) protocols amplify relatively small fragments precluding the use of this approach when examining gross rearrangements of DNA. By using combinations of DNA polymerases, which feature either good polymerase activity or error-correction abilities, it is now possible to extend the length of DNA fragment that can be amplified. These “long-PCR” protocols have allowed the development of more rapid and convenient ways to analyse large-scale rearrangements of DNA and in many cases has superseded alternative approaches such as Southern blotting. The protocol described in this chapter illustrates some of the key points to be considered when developing a long PCR protocol.