The cyst form of Toxoplasma gondii has been implicated as a cause of recrudescence of the latent infection in congenitally infected patients and in the immunocompromised host. A method was developed to evaluate the effect of drugs on the cyst form of the parasite and used to evaluate a variety of therapeutic agents. The most active compounds against the cyst form in vitro were arprinocid-N-oxide, azithromycin, and the hydroxynaphthoquinone 566C80.