A benznidazole-resistant population of Trypanosoma cruzi, Y strain, was selected after 25 successive passages (8 months) in mice treated with a single high drug dose. Initially, the resistant parasites produced a low parasitaemia level and low mortality rate in infected mice. Thereafter, the parasitaemia level and mortality rate increased to the same value obtained for mice infected with the wild-type strain. Long-term treatment with benznidazole (100 mg/kg/day) cured 71–80% of mice infected with the wild-type strain. No cure was observed in mice infected with the selected resistant parasite population. Treatment with 500 mg/kg of benznidazole at peak parasitaemia cleared all blood parasites from mice infected with wild-type parasites. No effect on parasitaemia level was observed in mice infected with the selected parasites. Benznidazole-resistant parasites showed cross-resistance to different drugs. Contrary to wild type, all clones analysed from the resistant T. cruzi population were resistant to benznidazole. Without drug pressure the resistance phenotype of clones was far more stable than that presented by the resistant population. This work demonstrates, for the first time, the in vivo selection of a population and clones of T. cruzi resistant to benznidazole, and makes available an experimental model for the study of mechanisms of drug resistance in T. cruzi.