Arbitrary primers have been used for the production of complex, PCR generated DNA profiles in order to undertake a preliminary random amplified polymorphic DNA (RAPD) analysis of strains (and related species) of two parasitic organisms that are responsible for important diseases endemic in Brazil: Schistosoma mansoni that causes schistosomiasis, and Trypanosoma cruzi that causes Chagas' disease. A relatively low level of polymorphism was found in S. mansoni when strains isolated from different regions of Brazil were compared, with less than 10% of bands exhibiting polymorphism. Comparison of different schistosome species, on the other hand, showed them to be distantly related with very few bands shared by even the more closely related species. Trypanosome strains were found to be much more variable. When strains were compared between zymodemes (groups of parasite strains with the same isoenzyme profiles), a maximum of 7% of bands were found to be common whereas among strains in the same zymodeme a clear characteristic pattern was observed. In the zymodeme most thoroughly studied, it was found that 59% of bands were shared. Band sharing analysis showed that the relationships of strains within a zymodeme correlate with their geographical origin and that the relationship between zymodemes correlates closely with that previously determined by isoenzyme analysis. These preliminary data indicate the ready applicability of RAPD analysis to the study of parasites where largely unexplored genetic variations may have an important bearing on the complexity and diversity of diseases.