Transcriptional regulation of transgenes depends upon genomic localization in higher eukaryotes. For the applied use of transgenic organisms as producers of pharmaceutically relevant proteins or as pest population control agents, a method to make transgene expression predictable is highly desirable. A targeting method that allows precise cassette replacement comprising solely genes of interest (without extraneous donor vector sequences) would be highly advantageous for insects and other multicellular organisms. In this report, we describe a method for transgene targeting to predefined chromosomal sites in Drosophila by using a transposon vector that, once integrated in the germ line, acts as an acceptor site for donor vectors. To make recombinational insertions irreversible, a FLP recombinase-mediated cassette exchange strategy was used, and to enhance donor-target pairing, a homing sequence from the linotte locus was used. Site-specific recombinants were screened by interconvertible eye fluorescence marker phenotypes yielding, on average, targeted insertions at a frequency of 23%. The cassette exchange system provides for repetitive integrations into the same locus, allowing comparative analysis of true transgenic alleles. Furthermore, this method was used to stabilize a targeted transgene by the postintegration excision of putatively mobile transposon sequences. The genomic targeting and stabilization strategy described for Drosophila should be applicable to other insects, specifically for the goals of optimizing heterologous protein expression and enhancing ecological safety of transgenic strains intended for release in biocontrol programs.homing sequence ͉ insect transformation ͉ recombinase-mediated cassette exchange ͉ transgene stabilization S ite-specific recombinases such as FLP, Cre, and ⌽C31 have emerged as powerful tools to manipulate genomes of eukaryotic model organisms (1). In mice, site-specific recombinase technology is being applied to modify chromosomal DNA in a spatially and temporally controlled manner, thereby bypassing embryonic lethality associated with many germ-line null alleles (2). In Drosophila, the FLP͞FRT (FRT, FLP recombinase target site) (3) has been extensively used to generate genetic mosaics in soma and germ-line (4), and chromosome rearrangements (5). Recently, systematic collections of molecularly defined deletions spanning Ͼ50% of the Drosophila melanogaster genome have been engineered by using FLP͞FRT (6, 7).Site-specific recombinase proteins catalyze the cutting and rejoining of two different DNA segments at specific target sequences. Depending on the relative orientation of the recombinase target sites, the outcome of a recombination reaction is excision and insertion of a circular DNA molecule, respectively, or inversion of intervening DNA. Excision of genomic DNA located between two equally oriented target sites is effectively irreversible due to the creation and, in dividing cells, loss of an episomal reaction product. In contrast, integration of a plasmid at a genomic...