A series of recent publications have firmly established the notion that Drosophila researchers now have a general method to subject genes for targeted modification by homologous recombination (HR) [Science 288 (2000) 2013; Genetics 157 (3),(2001) 1307; Genes Dev. 16 (12) (2002) 1568; Genetics 161 (2002) 1125-1136]. This method allows one to knockout essentially any gene starting with the DNA sequence of the gene. It has greatly enhanced studies of gene function as demonstrated by over 20 years of gene targeting practice in yeast and mouse. Here, I discuss the basic targeting methodology for eukaryotic organisms. I compare the Drosophila method with the traditional targeting scheme in yeast and mouse mainly to show that the targeting mechanism as well as many aspects of the experimental design remain unchanged, and that the Drosophila scheme differs only in the way in which the donor molecule for targeting is generated. I propose that the Drosophila method can be readily adapted in other organisms without culturable stem cells, since the mechanism for in vivo donor generation in Drosophila is likely to be functional in a variety of different organisms. (C) 2002 Elsevier Science (USA). All rights reserved.