The evaluation of the treatment for chronic Chagas disease faces the absence of any clear-cut criterion of cure. The low degree of parasitemia and the persistence of positive immunologic reactions represent some of the difficulties involved in addressing therapeutic efficacy. Our aim was to define whether PCR could be used as a laboratory method for evaluating cure in Chagas disease after specific treatment. We tested the utility of PCR amplification of the variable regions of minicircles from Trypanosoma cruzi kinetoplast DNA, in 76 xeno-positive chronic Brazilian patients who have been treated with benznidazole in Mambai (Goias State) and São Felipe (Bahia State). We observed a positive amplification result in only 25 out of 76 treated patients (33%). Therefore, the performance of one single PCR after therapy revealed parasite clearance in 67% of the treated individuals, while xenodiagnosis was negative in 84%. These observations suggest that PCR is the most sensitive technique available for direct detection of T. cruzi in chagasic patients and that it can be a very useful instrument for the follow-up of patients after specific chemotherapy. In this sense, we are now developing a quantitative approach based on the use of fluorogenic probes and real-time measurement of the amplification reaction (TaqMan technology) in order to precisely estimate the parasite load in chronic chagasic patients before and after treatment. This may be the basis for the future establishment of reliable criteria of cure for patients undergoing therapy.