The beginnings of Drosophila as a model organism reach far back into the 1900s to Thomas Hunt Morgan's first fly room. The success of this system for the study of genetics is closely linked to the fact that the fly is amenable to complex genetic manipulations so that random mutagenesis screens can be easily performed. Nonetheless, current advances in genomics and in our ability to predict protein function emphasize the importance of mutagenesis methods that are not random, but rather give the researcher control over how the gene is modified. Gene targeting in Drosophila, developed almost a decade ago, makes use of the organism's own DNA repair machinery to exchange genetic information between a chromosomal target and an exogenous template. Here we discuss available targeting methods and recent advances that facilitate repeated targeting and open the doors to routine allelic studies.