The most neglected aspects of Chagas disease (CD) have been patient care and treatment. Despite recent progress in the development of potentially improved drugs, there is no consensus among different research groups on the lack of therapeutic response markers to evaluate efficacy of newly proposed drugs early after treatment. A systematic review of current evidence regarding molecules which are potential biomarkers for therapeutic response has been conducted using quality assessment and target responses as primary criteria. The review provides a panorama of the cumulative evidence and specific needs for development of a battery of complementary biomarkers which together fulfill ideal or acceptable criteria to evaluate early responses to treatment for chronic CD. There are several marker candidates which together may fulfill acceptable criteria to indicate the efficacy of a trypanocidal treatment. Data from ongoing studies are considered essential to improve assessment of existing markers and to identify those for early follow-up of treated patients.