The life cycle of the apicomplexan parasite Toxoplasma gondii requires that an infectious cyst develop and be maintained throughout the life of the host. The molecules displayed on the parasite surface are important in controlling the immune response to the parasite. T. gondii has a superfamily of glycosylphosphatidylinositol (GPI)-anchored surface antigens, termed the surface antigen (SAG) and SAG-related surface antigens, that are developmentally regulated during infection. Using a clustering algorithm, we identified a new family of 31 surface proteins that are predicted to be GPI anchored but are unrelated to the SAG proteins, and thus we named these proteins SAG-unrelated surface antigens (SUSA). Analysis of the single nucleotide polymorphism density showed that the members of this family are the most polymorphic genes within the T. gondii genome. Immunofluorescence of SUSA1 and SUSA2, two members of the family, revealed that they are found on the parasite surface. We confirmed that SUSA1 and SUSA2 are GPI anchored by phospholipase cleavage. Analysis of expressed sequence tags (ESTs) revealed that SUSA1 had 22 of 23 ESTs from chronic infection. Analysis of mRNA and protein confirmed that SUSA1 is highly expressed in the chronic form of the parasite. Sera from mice with chronic T. gondii infection reacted to SUSA1, indicating that SUSA1 interacts with the host immune system during infection. This group of proteins likely represents a new family of polymorphic GPI-anchored surface antigens that are recognized by the host's immune system and whose expression is regulated during infection.Toxoplasma gondii is an obligate intracellular parasite and a member of the phylum Apicomplexa, which also includes Plasmodium, Cryptosporidium, Cyclospora, Eimeria, and Sarcocystis (3). T. gondii can reproduce both sexually and asexually. Sexual reproduction occurs only in the feline intestine and results in oocysts being shed in the feces. Within the environment, oocysts develop into infectious sporozoites. The asexual cycle has two developmental stages, namely, a rapidly replicating form called the tachyzoite and a slow-growing stage called the bradyzoite. Bradyzoites form tissue cysts in the central nervous system and muscle tissue and represent the chronic stage of infection. T. gondii is acquired orally either by ingestion of oocyst-contaminated foods or by eating undercooked, bradyzoite-harboring meat products. T. gondii infections in immunocompetent individuals are generally asymptomatic, but infections in immunocompromised individuals and fetuses are life-threatening (9).Despite its ability to reproduce sexually and its broad geographic range, T. gondii has a largely clonal population structure comprised principally of three lines (15,25). Analysis of genetic polymorphisms indicates that these three lines emerged from a single genetic cross approximately 10,000 years ago (27), establishing two major alleles for each locus (12). The type I lineage is highly virulent, with injection of one viable parasite being lethal to...