In total, 61 Chilean isolates of Trypanosoma cruzi, were analysed using schizodeme and Southern analysis, using as probes the highly variable regions of minicircles from cloned parasites. Isolates were collected and amplified from domestic and wild triatomines, and from infected subjects in all the endemic areas of Chile. Three major parasite genotypes could be detected in the domestic transmission cycle, whilst 1 major T. cruzi genotype is circulating in the wild transmission cycle. Schizodeme analysis suggested that T. cruzi isolates are mixed populations, whereas the Southern analyses detected only 3 mixed isolates using 4 selected minicircle segments as probes.