Isoenzyme and RFLP analyses were carried on freshly isolated Trypanosoma cruzi stocks and subsequent clones derived from patients with chronic Chagas disease. The isoenzymes separated the parasite stocks and clones in two groups: The stock hSLU239 (group I), isolated from a heart disease patient, showed the zymodeme 3 (Z3) profile (M. A. Miles et al., 1977, Transactions of the Royal Society of Tropical Medicine and Hygiene 71, 217-225). The stock mSLU142 (group II), isolated from a digestive disease (megaesophagus) patient, showed the Z2 profile. The parasite clones m1, m2, m3, and m4, derived from mSLU142, and clones h1 and h2, derived from hSLU239, showed isoenzyme profiles similar to those of Z2 and ZA (Miles et al. 1977; J. A. Romanha, 1982, Thesis, Universidade Federal de Minas Gerais). Furthermore, the T. cruzi clones derived from the cardiac disease patient differed from those derived from the megacolon patient in 3 of the 13 enzymes analyzed. RFLP analysis showed polymorphism at the EcoRI and PstI restriction fragments of the DNA sequences coding the glycolytic enzymes ALD, GPI, GAPDH, and PYK and separated the T. cruzi stocks and clones in three groups: I, comprising the stock hSLU239 and clone m4, which was classified as homozygous CC, BB, AA, and AA for the ALD, GPI, PYK, and GAPDH genes, respectively; II, formed by the parasite stock mSLU142 and clones h1 and h2 (derived from hSLU239), which was classified as homozygous AA, AA, CC, and BB for ALD, GPI, PYK, and GAPDH genes, respectively . These findings show that the infection of each Chagas disease patient may be produced by genetically diverse mixed parasite populations.