The Cre-LoxP system is widely used to create conditional knockout strains. This whitepaper provides basic terminology and describes specific genotyping issues surrounding the Cre-LoxP system. In the Cre-LoxP system the genetic sequence of the organism has been modified to introduce at least two artificial LoxP sites. When this organism is mated with one that has had a Cre Recombinase artificially introduced into it, the region between the LoxP site is removed. Detecting the floxed and recombined alleles involve different strategies.