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Q fever is a zoonotic disease caused by the bacterium Coxiella burnetii. Clinical presentation in humans varies from asymptomatic to flu-like illness and severe sequelae may be seen. Ruminants are often sub-clinically infected or show reproductive disorders such as abortions. In Egypt, only limited data on the epidemiology of Q fever in animals are available. Using a stratified two stage random sampling approach, we evaluated the prevalence of Coxiella burnetii specific antibodies among ruminants and camels in 299 herds. A total of 2,699 blood samples was investigated using enzyme-linked-immunosorbent assay (ELISA). Coxiella burnetii specific antibodies were detected in 40.7% of camels (215/528), 19.3% of cattle (162/840), 11.2% of buffaloes (34/304), 8.9% of sheep (64/716) and 6.8% of goats (21/311), respectively. Odds of seropositivity were significantly higher for cattle (aOR: 3.17; 95% CI: 1.96-5.13) and camels (aOR: 9.75; 95% CI: 6.02-15.78). Significant differences in seropositivity were also found between domains (Western Desert, Eastern Desert and Nile Valley and Delta) and 25 governorates (p < 0.001), respectively. Animal rearing in the Eastern Desert domain was found to be a significant risk factor (aOR: 2.16; 95% CI: 1.62-2.88). Most seropositive animals were older than four years. No correlation between positive titers and husbandry practices or animal origin were found (p > 0.05). Only 8.7% of the interviewed people living on the farms consumed raw camel milk and none reported prior knowledge on Q fever. Findings from this nationwide study show that exposure to Coxiella burnetii is common in ruminants and camels. Disease awareness among physicians, veterinarians and animal owners has to be raised. Future epidemiological investigations have to elucidate the impact of Q fever on human health and on the economy of Egypt.