Q fever is an almost ubiquitous zoonotic disease with a worldwide distribution, caused by Coxiella burnetii which can infect different types of animal species such as cattle, sheep and goats, as well as humans. Infection with C. burnetii in small ruminants, are mostly sub-clinical, although, abortions and stillbirths can occur. The aim of this study was to provide molecular evidence of C. burnetii in aborted small ruminants in different districts of Sulaimani province, Kurdistan-Iraq. Blood and faecal samples were collected from 180 aborted sheep and goats (90 samples each) and analyzed by conventional Polymerase Chain Reaction (PCR) for DNA detection of transposase gene (IS1111) of C. burnetii from February to June 2019. (Comparison sequence analysis exhibit that field isolates highest identities of (Iraq, Iran and China) strains with the rate of 99.84%). Shedding of C. burnetii by aborted sheep and goats was found only in (5.55%) faecal samples investigated. Only 10 out of 60 faecal samples (16.66%) were positive. Six out of 48 faecal samples (12.5%) and 5 out of 12 faecal samples (41.66%) were positive in aborted sheep and goats respectively. None of the blood samples revealed positive amplification for C. burnetii DNA. This paper documents the first molecular detection of C. burnetii in aborted small ruminants in Sulaimani province Kurdistan-Iraq.