Background: Cryptosporidiosis is one of the most important problems among neonatal ruminants. Cryptosporidium parvum is the agent causing the disease. Cryptosporidium infection, responsible for diarrhea, dehydration, weight loss and death in neonatal ruminants, leads to significant economic losses for producers. In calves naturally or experimentally infected with cryptosporidiosis, many agents have been reported to have therapeutic and protective effects. The objective of this study was to compare the effectiveness of halofuginone lactate and paromomycin in the treatment of calves naturally infected with Cryptosporidium parvum.