As with other organisms with a completed genome sequence, opportunities for performing large-scale studies, such as expression and localization, on Toxoplasma gondii are now much more feasible. We present a system for tagging genes endogenously with yellow fluorescent protein (YFP) in a ⌬ku80 strain. Ku80 is involved in DNA strand repair and nonhomologous DNA end joining; previous studies in other organisms have shown that in its absence, random integration is eliminated, allowing the insertion of constructs with homologous sequences into the proper loci. We generated a vector consisting of YFP and a dihydrofolate reductasethymidylate synthase selectable marker. The YFP is preceded by a ligation-independent cloning (LIC) cassette, which allows the insertion of PCR products containing complementary LIC sequences. We demonstrated that the ⌬ku80 strain is more effective and efficient in integrating the YFP-tagged constructs into the correct locus than wild-type strain RH. We then selected several hypothetical proteins that were identified by a proteomic screen of excreted-secreted antigens and that displayed microarray expression profiles similar to known micronemal proteins, with the thought that these could potentially be new proteins with roles in cell invasion. We localized these hypothetical proteins by YFP fluorescence and showed expression by immunoblotting. Our findings demonstrate that the combination of the ⌬ku80 strain and the pYFP.LIC constructs reduces both the time and cost required to determine localization of a new gene of interest. This should allow the opportunity for performing larger-scale studies of novel T. gondii genes.Toxoplasma gondii is an obligate intracellular protozoan in the phylum Apicomplexa that has garnered more intense study in recent decades. This is due in part to the genetic tractability and ease of growth of T. gondii and also because knowledge obtained for this parasite is often relevant to its kin, including other pathogens of medical and veterinary importance, such as Plasmodium falciparum, the parasite that causes malaria (11). The genome sequence of Toxoplasma was recently completed (10), opening the door to identifying novel genes involved in a variety of events, such as cell invasion, replication, gliding motility, metabolism, stage conversion, and virulence. With a large number of new genes of interest, it is essential to have tools that enable investigators to perform studies on a larger scale. One bottleneck for the analysis of novel genes is protein localization, since this generally necessitates time-consuming production of antibodies that often require additional affinity purification. Protein localization by ectopic expression of a tagged construct can also be problematic due to overexpression or mistiming of expression from a heterologous promoter. If genes could be tagged directly on the chromosome, this would better mimic natural expression and allow the use of fluorescent protein tags or standardized antibodies to monitor localization.DNA double-strand breaks...