Since medium chain fatty acids (MCFAs) and their derivatives exert antimicrobial activities, their potential in controlling alimentary protozoa was examined in 12 calves infected with coccidia. Medium chain triglyceride (MCT), esterified fat of MCFAs, was administered into the rumen of 6 calves using an esophageal tube and into the abomasum of another 6 calves to ensure intestinal delivery by the function of the reticular groove reflex. Abomasal MCT inhibited the shedding of coccidial oocysts with less toxicity on ruminal protozoa. Conversely, intraruminal MCT showed negligible anticoccidial effect but toxicity on ruminal protozoa (defaunation). The anticoccidial efficacy was confirmed by abomasum feeding of MCT and not into the rumen. The results shed light on dietary fats for coccidial control.