Although there has been an improvement in the diagnosis of chronic Chagas' disease, the low sensitivity of indirect parasitological tests is a drawback to its application in diagnosis and post-therapeutic control. Polymerase chain reaction (PCR) has limited use in routine diagnosis due to the need of specific laboratory facilities, common DNA cross-contamination, and high costs. At the same time, the high variability of PCR results found in different regions of Brazil raises some questions concerning its applicability for diagnosis. PCR's high specificity is indicative that it can be used as a confirmation method in inconclusive serology diagnosis as well as an auxiliary method in pos-therapeutic control of chronic Chagas' disease when comparing to serology and parasitological techniques. It is discussed here the applicability of molecular and indirect parasitological methods in the diagnosis and post-therapeutic control of chronic Chagas' disease based on the literature published from 1954 to 2001.