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Chagas disease, caused by the parasite Trypanosoma cruzi, affects over 6 million people, mainly in Latin America. Two different clinical phases, acute and chronic, are recognised. Currently, 2 anti-parasitic drugs are available to treat the disease (nifurtimox and benznidazole), but diagnostic methods require of a relatively complex infrastructure and trained personnel, limiting its widespread use in endemic areas, and the access of patients to treatment. New diagnostic methods, such as rapid tests (RDTs) to diagnose chronic Chagas disease, or loop-mediated isothermal amplification (LAMP), to detect acute infections, represent valuable alternatives, but the parasite's remarkable genetic diversity might make its implementation difficult. Furthermore, determining the efficacy of Chagas disease treatment is complicated, given the slow reversion of serological anti-T. cruzi antibody reactivity, which may even take decades to occur. New biomarkers to evaluate early therapeutic efficacy, as well as diagnostic tests able to detect the wide variety of circulating genotypes, are therefore, urgently required. To carry out studies that address these needs, high-quality and traceable samples from T. cruzi-infected individuals with different geographical backgrounds, along with associated clinical and epidemiological data, are necessary. This work describes the framework for the creation of such repositories, following standardised and uniform protocols, and considering the ethical, technical, and logistic aspects of the process. The manual can be adapted according to the resources of each laboratory, to guarantee that samples are obtained in a reproducible way, favouring the exchange of data among different work groups, and their generalizable evaluation and analysis. The main objective of this is to accelerate the development of new diagnostic methods and the identification of biomarkers for Chagas disease. Author summary: The diagnosis of Chagas disease requires costly equipment and trained personnel, which unavailability hinders access to diagnosis, and treatment, in vast areas of endemic regions. Additionally, timely assessment of treatment efficacy is complicated due to the slow reversion of serological anti-T. cruzi reactivity. Hence, there is an urgent need for biomarkers of early therapeutic efficacy and disease prognosis, as well as more practical diagnostic tools. To conduct studies that can address these needs, it is essential to have collections of clinical samples with good quality, traceability, and appropriately associated clinical-epidemiological information. In this work, we provide a standard protocol to collect, process, store, and transport clinical samples from Chagas disease patients. The manual was produced upon reaching a consensus among the experts within the NHEPACHA network, a coalition of clinical and academic researchers from the Americas and Spain that pursues the identification and validation of new biomarkers and diagnostics for Chagas disease. [ABSTRACT FROM AUTHOR]