Bacterial abortive agents such as Brucella spp., Salmonella spp., Campylobacter spp., Listeria spp. cause serious infections that lead to significant economic losses in cattle and sheep breeding. These bacteria can be easily cultured under in vitro laboratory conditions. Abortions caused by intracellular bacteria such as Coxiella burnetii (C. burnetii), Chlamydophila abortus (C. abortus) and Francisella tularensis (F. tularensis) are less prevalent in abortive cases and the diagnosis of these bacteria, many of which need to cell culture for cultivation and biosafety level-3 laboratory facilities for safe working, can be made by PCR. In this study, it was aimed to determine the molecular prevalence of C. burnetii, C. abortus and F. tularensis agents, which were neglected during the diagnosis of abortions, in cattle and sheep collected from different regions of Turkey. A total of 395 clinical materials were analyzed via agent-specific commercial Real-Time PCR. As a result, the molecular prevalence of F. tularensis, C. burnetii and C. abortus was determined as 14%, 2.9% and 2.28%, respectively. F. tularensis in cattle clinical samples and C. burnetii in sheep clinical samples were not found. This is the first report that F. tularensis was found as an agent in an abortive material in Turkey. Although it differs in terms of prevalence, it has been determined that these microorganisms, which are neglected in routine diagnosis, can be spread with aborted materials, especially vaginal discharge, which may pose a risk of transmission.