Reverse genetics in Plasmodium, the genus of parasites that cause malaria, still faces major limitations. Only red blood cell stages of this haploid parasite can be transfected. Consequently, the function of many essential genes in these and subsequent stages, including those encoding vaccine candidates, cannot be addressed genetically. Here, we establish conditional mutagenesis in Plasmodium by using site-specific recombination and the Flp͞FRT system of yeast. Site-specific recombination is induced after cross-fertilization in the mosquito vector of two clones containing either the target sequence flanked by two FRT sites or the Flp recombinase. Parasites that have undergone recombination are recognized in the cross progeny through the expression of a fluorescence marker. This approach should permit to dissect the function of any essential gene of Plasmodium during the haploid phase of its life, i.e., during infection of salivary glands in the mosquito and infection of both the liver and red blood cells in the mammal.A ll symptoms and complications of malaria are caused by the multiplication of Plasmodium parasites inside the red blood cells (RBC) of a host. The parasite is transmitted between two mammalian hosts through mosquitoes, typically Anopheles, during blood feeding (Fig. 1). It is ingested as sexual forms (gametocytes), and fertilization occurs rapidly in the lumen of the mosquito midgut. It is then inoculated to a new mammalian host as haploid sporozoites, which transform inside hepatocytes into forms that invade RBC.Genome manipulation is an essential tool for understanding key events in the Plasmodium life cycle in molecular terms. Stable transfection of the parasite (1, 2) and modification of its genome by homologous recombination (3-5) are now common procedures. The genome, however, can be manipulated only in RBC stages of the parasite, which are the only stages that can be produced in large amounts and subjected to selection. An important limitation of the current technology is that loss-offunction mutations cannot be selected in genes that play a role in parasite invasion of, or multiplication inside RBC, which are required for selection. Although evidence can be gained that a gene is important for the RBC cycle when its disruption cannot be selected, as has been reported for the leading vaccine candidates merozoite surface protein 1 (MSP-1) (6) and apical membrane antigen 1 (AMA-1) (7) and many other proteins (8), the actual function of the protein cannot be studied in the RBC or subsequent stages. Likewise, an increasing proportion of Plasmodium proteins are recognized as being produced at more than just one parasite stage, and gene inactivation in RBC stages can only reveal their earlier role in the cycle. Therefore, conditional procedures are needed for inactivating or activating genes at will during the Plasmodium life cycle.Site-specific recombination (SSR) offers an effective way to inactivate a gene in a temporally defined manner. Two SSR systems have been widely used in eukaryotes, Cre͞...