Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) at eight independent loci was used to determine the types (I, II or III) lineage of 20 Toxoplasma gondii strains isolated from humans and animals in Brazil. RH (type I, highly virulent), ME49 (type II, avirulent) and VEG (type III, avirulent) were used as reference strains. Differently from expected frequencies, all Brazilian strains showed to have recombinant genotypes, with typical alleles of types I, II or III at almost all loci assessed. The cB21-4 locus, a microsatellite marker, showed a higher allelic polymorphism with seven alleles among strains under analysis. Data have also shown that many Brazilian T. gondii strains presented a new haplotype at the L363 locus. When results of the eight loci were combined, 14 schizodemes were characterized out of the 20 T. gondii strains isolated in Brazil. The phenogram representing PCR-RFLP data separated Brazilian strains into two distinct genetic groups associated with murine virulence phenotype, termed groups I-A and I-B. Strains from group I-A (AS28, BV and N) that were highly virulent in BALB/c mice, were clustered with RH reference strain. Only those strains presented the haplotype I at the L363 locus, suggesting that this could be a possible marker of highly virulent strains. Strains from group I-B (cystogenic strains) showed a more heterogeneous behavior regarding virulence: a few of them (EGS, RAR, SAF, D5 and D6) were virulent, others (C4, P and D8) avirulent and most of them (D1, D2, D3, D4, D7, EFP, CH1, CH2 and CH3) intermediate virulent in mice. A significant linkage disequilibrium was observed in the population surveyed. However, the role of sexual recombination in the population structure of T. gondii in Brazil seems to be more central than in Europe and North America, where most studies have been performed.