30 Trypanosoma cruzi strains isolated from chronic chagasic patients were studied at the genotype level by RAPD with arbitrary primers and SSR-PCR analysis. The genetic distance of strains was measured by the percentage of unshared bands. The results showed that the strains isolated from chronic patients from different Chagas' disease endemic areas of Brazil constituted a broad group significantly more correlated than reported in previous studies, presenting RAPD profiles with an average of 71% of shared bands and SSR-PCR patterns with a mean of 59% of shared bands. In contrast to other findings in the literature, these strains did not group on the basis of their geographic origin. These results suggest that a special adaptation of a parasite population in human hosts from mixed infective T. cruzi populations circulating in nature may have occurred.