In Drosophila, genetic techniques relying on stochastic chromosomal rearrangements involve the generation and screening of a large number of fly stocks to isolate a few lines of interest. Here, we describe a PCR-based method allowing non-lethal molecular characterization of single flies. Using this procedure, individual candidate recombinant animals can be genotyped and selected one generation earlier than with extant methodology and, importantly, before stocks are established. This advance should significantly facilitate several of the most fundamental and routine techniques in Drosophila genetics.