Chagas disease is considered a public health issue, especially in Latin America. To this date, the course of the infection caused by the parasite is yet to be completely understood and the conventional treatment do not promote a cure in the chronic phase, meaning there is an urgent need to discover new drugs. The expression of reporter genes by transgenic parasites has become an important tool in the screening of new compounds, whether in the study of the parasite, in the development of and assays, or in the application of High-Throughput Screening utilizing compounds collections. This review sought to gather information about transgenic applications in screening studies of compounds with action specifically against Chagas disease, the reporter genes in use, besides the highlighted characteristics of each one by the literature, including the performed assays, evolutionary forms and techniques applied, aiming to facilitate the identification of the reporter gene system or research model whose characteristics best adapt to the needs of new studies, contributing to the decisions about a framework adaptable to the reality of laboratories, in the screening of potentially trypanocidal compounds.