Q fever, a universal zoonotic disease, is caused by Coxiella burnetii. Dogs are considered as a reservoir of this bacterium and can infect people and other animals by shedding this pathogen in excretions. In this study, we determine the existence of the causative agent of Q fever in the uterine samples of dogs attending to the veterinary animal hospital of Shahid Bahonar University of Kerman. Specimens were collected and assessed for the presence of C. burnetii by nested Trans-PCR. C. burnetii was molecularly identified in 5 out of 41 (12.1%) collected samples. This study is the first known identification of C. burnetii in the uterine of dogs in Kerman, Iran. According to our findings, dogs should be considered as an important source of this zoonotic pathogen. Detection of C. burnetii in uterine samples emphasizes the need for the further investigations on Q fever in small animals in this area.