Previous studies have shown a high prevalence of toxoplasmosis and the frequent occurrence of ocular disease in Brazil. To identify the genotypes of parasite strains associated with ocular disease, we compared 25 clinical and animal isolates of Toxoplasma gondii from Brazil to previously characterized clonal lineages from North America and Europe. Multilocus nested polymerase chain reaction analysis was combined with direct sequencing of a polymorphic intron to classify strains by phylogenetic methods. The genotypes of T. gondii strains isolated from Brazil were highly divergent when compared to the previously described clonal lineages. Several new predominant genotypes were identified from different regions of Brazil, including 2 small outbreaks attributable to foodborne or waterborne infection. These findings show that the genetic makeup of T. gondii is more complex than previously recognized and suggest that unique or divergent genotypes may contribute to different clinical outcomes of toxoplasmosis in different localities.