To determine the prevalence of the 3 primary clonal lineages of Toxoplasma gondii (strain types I, II, and III) in a potential food source of infection for humans, we analyzed 43 isolates of T. gondii that had been collected from pigs at an abattoir in Iowa. Parasites were harvested as in vitro-grown tachyzoites, and their genotypes were determined at the SAG1 and SAG2 loci. On the basis of the allele identified at the SAG2 locus, isolates were grouped into 1 of the 3 primary lineages. Type II strains were by far the most prevalent, accounting for 83.7% of the isolates. The type III genotype was identified in only 16.3% of the isolates. These prevalences differ significantly from a previous sampling of isolates from animals but are similar to the frequencies with which they occur in human disease cases. Similar to the previously characterized strain P89, strains P62 and P105 appeared to have recombinant genotypes. The type I genotype was not identified in the isolates from pigs although these strains have previously been shown to account for approximately 10-25% of toxoplasmosis cases in humans.