The intranuclear coccidian parasite of Testudines (TINC) is an emerging pathogen of tortoises. Three captive red-footed tortoises (Chelonoidis carbonaria) from an isolated collection presented with multiple acute, nonspecific clinical signs. One tortoise died and was diagnosed with intranuclear coccidiosis on histopathology with confirmation by quantitative polymerase chain reaction (qPCR). In addition to tissues where TINC has been previously described, coccidia were identified in the pineal gland, choroid plexus, and testicular Sertoli cells. The two remaining tortoises survived after treatment with oral ponazuril (20 mg/kg every 48 hr for 56 days) and remained asymptomatic, although not cleared of infection, for 21 months, as the number of coccidian gene copies detected by qPCR was reduced in one tortoise. This report extends the known host range of this parasite to continental South American tortoises, describes new sites of infection by histopathology, and has management implications for this disease.