Background: During the colonial period, the indigenous saraguros maintained their traditions, knowledge, and practices to restore and preserve the health of their members. Unfortunately, many of their practices and medicinal resources have not been documented. In this study, we sought to document the traditional healers’ (yachakkuna saraguros) knowledge about medicinal and psychoactive plants used in the mesas and in magical-religious rituals. The study was conducted under a technical and scientific cooperation agreement between the Universidad Técnica Particular de Loja (UTPL), the Dirección Provincial de Salud de Loja (DPSL), and the Saraguro Healers Council (Consejo de Sanadores de Saraguro). Methods: For the present study, the DPSL and Saraguro Healers Council selected the 10 yachakkuna most recognized for their knowledge and their use of sacred and psychoactive species. Ten interviews with the selected yachakkuna were conducted between 2010 and 2011 to ascertain how the Saraguro traditional healing system is structured and to obtain a record of the sacred and medicinal plant species used to treat supernatural diseases and for psychoactive purposes. Results: The present study describes the traditional health system in the Saraguro indigenous community located in southern Ecuador. It also describes the main empirical methods used to diagnose diseases: direct physical examination of the patient, observation of the patient’s urine, documentation of the patient’s pulse, limpia, palpation and visionary methods, including supernatural diseases (susto, vaho de agua, mal aire, mal hecho, shuka) and reports of the use of sacred and medicinal psychoactive plants, such as the San Pedro cactus (Echinopsis pachanoi), wandug (Brugmansia spp.), and tobacco (Nicotiana spp.). This study also describes the rituals (limpia, soplada) employed by the Saraguro yachakkuna to treat supernatural diseases. Finally, we report on the main plants used during limpia in the Saraguro community. Conclusion: The current traditional health system in the Saraguro community is the cultural expression of the Saraguros’ presence as an Andean group in southern Ecuador: it represents their character as indigenous group, their ability to survive as a community despite strong external pressure, and the desire to maintain their ancient healing heritage. Keywords: San Pedro cactus, Medicinal plants, Saraguro, Psychoactive plants, Yachakkuna, Healing rituals