Isozyme analysis (12 enzymes: 14 loci) was conducted on 99 isolates of Trypanosoma cruzi: 77 from Guatemala, 5 from Mexico and 17 from South American countries. Analyses of 4 population-genetic indices were undertaken to assess the possibility of genetic exchange occurring among Guatemalan isolates. The results provide evidence for a degree of genetic exchange occurring among isolates from this relatively small geographical area. Previous studies of population genetics on T. cruzi might have failed to detect this phenomenon because they tended to use isolates originating far from one another, rendering gene exchange unlikely for geographical reasons. Phylogenetic data, presented here, show considerable differences in genetic structure between Central and South American isolates, suggesting that different biological and clinical properties might be expected. For example, there are differences in clinical syndromes between Central and South America, a situation discussed further here.