Coxiella burnetii is a causative agent of Q fever which is highly infectious zoonotic disease. C. burnetii has become one of the most important causes of abortion in livestock, which can lead to widespread abortions in these animals. There are very limited studies on the prevalence of C. burnetii infection in cases of animal abortion in Iran. The aim of this study was to investigate C. burnetii in livestock abortion samples in Iran. Abortion samples from cattle, sheep and goat were collected from different parts of Iran and were tested using Real-time PCR targeting IS1111 gene of C. burnetii. In this study, 36 samples (24.66%) of the 146 collected samples were positive for C. burnetii. The prevalence of C. burnetii was 21.78% (20 of 94 samples) in sheep samples. Also, 10 of 46 cattle samples (21.74%) were positive. All six goat abortion samples were positive for C. burnetii. The findings of the study demonstrate that C. burnetii have important role in livestock abortions in Iran and more attention should be paid to Q fever by the health care system and veterinary organization.