Diagnostic methods for Chagas disease rely primarily on serological and molecular tests to detect anti-T cruzi antibodies or parasite-derived DNA. However, these tests do not predict clinical outcomes or treatment responses, as serological results may take years to turn negative, making them impractical for monitoring treatment progress. Molecular tests, though highly sensitive, can identify parasites but cannot rule out the presence of dormant forms or low levels of parasitemia, which may later reactivate. Due to the lack of reliable biomarkers for disease prognosis and treatment monitoring, there has been growing interest in host-derived markers as alternatives. One area of focus is the hypercoagulability observed in T. cruzi-infected individuals, which increases the risk of thrombotic events due to factors like chronic inflammation, dysregulation of immunothrombosis, and vasculitis. In addition, extracellular vesicles (EVs), i.e., double-membrane-enclosed particles found in various biological fluids, have emerged as a potential source of biomarkers for disease detection, prognosis, and monitoring. EVs contain proteins, lipids, and nucleic acids that can provide valuable molecular information about a patient’s condition. This chapter outlines procedures for detecting host-derived biomarkers of Chagas disease, particularly those related to hypercoagulability, such as F1 + 2 and endogenous thrombin potential assays, and the isolation and characterization of EVs as biomarkers for response to treatment and disease progression.