Caribou are keystone species important for human harvest and of conservation concern; even so, much is unknown about the impact of parasites on caribou health and ecology. The aim of this study was to determine the seroprevalence, tissue prevalence, and diversity of tissue-dwelling coccidian parasites (including Toxoplasma gondii, Neospora caninum and Sarcocystis spp.) in 88 migratory caribou (Rangifer tarandus) harvested for human consumption in two communities in Nunavik, Quebec, Canada. Both T. gondii and N. caninum have potential to cause abortions and neurological disease in caribou. Seroprevalence for antibodies to T. gondii using ELISA on fluid from thawed hearts was 18% overall, and no DNA of T. gondii was detected in tissues, which has positive implications for food safety since this parasite is zoonotic. Seroprevalence for antibodies to N. caninum using competitive ELISA was 5%, and DNA of N. caninum was detected in only one heart sample. DNA of Sarcocystis, a non-zoonotic, related coccidian, was detected in tissue samples from 85% of caribou, with higher prevalence in heart (82%) than skeletal muscle (47%). This is the first time that Sarcocystis spp. from caribou in Canada have been identified to species level, many of which have been described in reindeer from Fennoscandia. The high prevalence and diversity of Sarcocystis spp. suggests intact trophic relationships between canids and caribou in Nunavik. Besnoitia spp. was serendipitously detected in three muscle samples, a parasite previously associated with skin lesions in caribou in Nunavik. Community-level differences in T. gondii exposure and prevalence of Sarcocystis spp. in skeletal muscle tissues may reflect differences in hunter selection of individual animals and muscles, or possibly regional differences in the ecology of carnivore definitive hosts for these parasites. Further work is needed to explore effects of tissue coccidians in caribou, their taxonomic classifications, and community level differences in parasite prevalence and diversity.