This chapter describes methodologies for both forward genetics—(i.e., conventional and transmission genetics) and reverse genetics (transfection/transformation). The study of parasitic protozoa has benefited relatively little from the application of genetics. In part, this is because most of the organisms that have been models for biochemical and molecular analyses do not lend themselves to such approaches. In many cases, no sexual cycle is known and culture methods are so cumbersome that in vitro manipulations are extremely difficult. One exception to both these limitations is the apicomplexan protozoan, Toxoplasma gondii. It has long been known that toxoplasma is capable of unlimited asexual growth as a haploid form in almost any warm-blooded vertebrate. The inherent potential for using genetics to understand the biology of toxoplasma is now beginning to be realized. There is, however, much to be done. Among the major challenges are the development of stable plasmid replicons, physical maps of chromosomes, more detailed genetic maps, sequence tag sites or similar efficient, high density markers, catalogued cosmid or yeast artificial chromosome banks that allow moving from a given genetic location direction to the genomic region of interest, and methods for in vitro crosses.