Crimean Congo hemorrhagic fever (CCHF) is a viral zoonotic disease. During 1999–2011, 871 human cases of CCHF were diagnosed in Iran. A history of serologic conversion for CCHF virus was seen in 58.7% of 2,447 sheep samples, 25.0% of 1,091 cattle samples and 24.8% of 987 goat samples from different parts of Iran. Spatial analysis showed that the main foci of this disease in humans during these years were in eastern Iran (P< 0.01) and the second most common foci were in northeastern and central Iran. Two livestock foci were detected in the northeastern northwestern Iran. On the basis of the results of this study, infection likely entered Iran from eastern and western neighboring countries.