To facilitate genotyping of Toxoplasma gondii in vitreous fluid of patients with severe or atypical ocular toxoplasmosis, polymerase chain reaction (PCR) restriction fragment length polymorphism (RFLP) assays were developed for SA G3 (p43) and SAG4 (p18), 2 single-copy surface antigen genes. Together with strategies for S A G1, S A G2, and B1, multilocus RFLP analyses were performed on PCR-amplified parasite DNA present in 12 clinical specimens. Most samples (8/12) were not infected by type II or type III mouse-avirulent strains. Only 1 type III and 3 type II strains were identified, all from immunosuppressed patients. In 6 otherwise healthy adults and in 1 immunosuppressed patient, the S A G1 allele associated with mouse virulence was amplified. Of 12 samples, 3 possessed true type I strains; 5 of 12 had new recombinant genotypes with alleles typical of type I or III strains at all loci examined. The unusual bias toward type I and/or recombinant genotypes bearing the SA G1 type I allele associated with mouse virulence in immunocompetent adults has important implications for the epidemiology and efficacious treatment of ocular toxoplasmosis.