Dromedary camels (Camelus dromedarius) are raised in extremely strict ecological conditions of deserts. Camels are vulnerable to many zoonotic infections. There are limited data on the occurrence of Q fever and borreliosis in camels, in Iran. The current study was focused on the occurrence of Coxiella burnetii and Borrelia spp. infection in the blood samples of Iranian camels using molecular assays. Effect of the presence of these infections on various hematological factors and some acute-phase proteins (Hp, a1AGP, SAA) were also investigated. Blood samples were collected from 113 clinically healthy camels to investigate the presence of the infections using nested PCR. Moreover, the sequence of positive samples was analyzed phylogenetically. Routine haematological tests were performed and the concentrations of acute-phase proteins were measured in serum using enzyme immunoassay. PCR result showed that 6.19% (95% CI: 2.53-12.35%) (7/113) of camels were positive for C. burnetii. In addition, sequencing results of the corresponding gene of the outer membrane protein (com1) revealed two different genotypes of C. burnetii agent in camels from Southern Iran. In the PCR assay, Borrelia spp. DNA was not detected in the samples. No significant difference was observed in hematological parameters or acute-phase proteins between positive and negative Q fever camels except for mean corpuscular hemoglobin (MCH) and red cell distribution width (RDW). Clinically healthy camels might be very important reservoirs of zoonotic pathogens. Q fever is not considered a notifiable disease in camels of Iran, and clinical cases may scarcely be recognized by the healthcare system. Due to a lack of adequate information, additional studies on the molecular epidemiology and clinical pathology aspects of C. burnetii infection in Iran are needed.