Sarcocystis spp., Neospora spp., and Toxoplasma gondii are Apicomplexa protozoa that can infect horses. This study aimed to investigate the occurrence of antibodies against Sarcocystis spp., Neospora spp., and T. gondii in horses slaughtered in southern Brazil. The presence of histological lesions, tissue cysts, and Sarcocystis spp. DNA in the hearts of these horses was also investigated. A total of 197 paired serum and heart samples were evaluated by serology and direct microscopic examination; 50 of these samples were subjected to histopathological and PCR analyses. Antibodies against at least one of the protozoa were detected in 146 (74.1%) of the serum samples. The frequencies of positive serology were: 36% (71/197) against Sarcocystis spp., 39.1% (77/197) against Neospora spp., and 47.2% (93/197) against T. gondii. No cysts, Sarcocystis spp. DNA, or histopathological lesions were observed in myocardial tissue samples. The frequencies of antibody seropositivity against Sarcocystis spp., Neospora spp., and T. gondii showed that horses are frequently infected by these parasites in southern Brazil. The absence of sarcocysts in horse tissues is compatible with their role as aberrant/accidental hosts in the life cycle of Sarcocystis spp..