The amplification of transposon insertion flanking sequences is the basis of a variety of techniques used for the detection and characterization of specific transposon insertion events. We have developed a method for the efficient size determination and quantification of amplified genomic sequences that flank Mutator (Mu) transposon insertions in maize. Using this detection method, we have been able to optimize Mu insertion site amplification and to assess amplification from increasingly complex templates representing increasing numbers of Mu-active maize plants. This detection method should be applicable for the characterization of transposon or transgene insertion events in a wide variety of organisms.