Trypanosoma cruzi populations are subdivided into natural clones that can exhibit considerable genetic differences. It has been proposed that T. cruzi clonal structure has a major impact on this parasite's biological properties. The present work aims at testing this hypothesis. Twenty-one stocks isolated from various ecological cycles, places, and hosts were characterized by multilocus enzyme electrophoresis (MLEE) with 22 genetic loci and random amplification of polymorphic DNA (RAPD) with 10 primers on the one hand and by 14 different biological parameters on the other hand. These parameters were related to: (i) growth kinetics of epimastigotes and amastigotes; (ii) infection of culture cells by amastigotes; (iii) viability of extracellular trypomastigotes; or (iv) sensitivity of epimastigotes, trypomastigotes, and amastigotes to Benznidazole and Nifurtimox. MLEE and RAPD results exhibited parity to each other, as previously noted (M. Tibayrenc, K. Neubauer, C. Barnabé, F. Guerrini, D. Skarecky, and F. J. Ayala, 1993, Proceedings of the National Academy of Sciences of the USA 90, 1335-1339), and showed that the 21 stocks were distributed into three main genetic groups, 19/20, 32, and 39, corresponding to the major clones 19, 20, 32, and 39 previously described on the basis of 15 isozyme loci. Most biological parameters showed a strong correlation to the genetic distances evaluated from either MLEE or RAPD, which favors the working hypothesis. The only exception came from drug sensitivity estimated on trypomastigote forms. The overall results made it possible to firmly reject the null hypothesis that there is no relationships between evolutionary distances and biological differences in T. cruzi natural clones.