Diarrhea is a multifactorial symptom of infectious agents, nutritional and environmental factors. Although many prevention and treatment strategies have been developed to prevent diarrhea, diarrhea is still one of the most common problems in ruminants. Cryptosporidiosis, coccidiosis and giardiasis in newborns and young ruminants are important protozoer diseases causing diarrhea. Although the symptomatic treatment of neonatal diarrhea is similar, there are differences in the etiologic treatment. In this review, antiprotozoal drugs used in the treatment of cryptosporidiosis, coccidiosis and giardiasis are discussed.