Coxiella burnetii is a Gram-negative bacterium capable of infecting a wide range of hosts. Even though domestic ruminants are the main reservoirs, wild animals can also play this role, being the source of some documented human outbreaks. In farm animals, it is associated with reproductive disorders, while in humans, it causes Q Fever, a febrile illness that can progress to endocarditis, vascular complications, and persistent infections. Although most cases are asymptomatic, it is essential to track infected animals, as even in the absence of clinical signs, they can shed the pathogen, facilitating transmission and posing a significant risk to human and livestock health. This study screened 182 birds from 11 distinct orders at a wildlife rehabilitation center. Oral and cloacal swabs were collected for DNA extraction and subsequent analysis by real-time PCR (qPCR) using specific primers and a probe targeting the IS1111 gene of C. burnetii. Results identified C. burnetii DNA in 1.6% (3/182) of the subjects. Positivity was confirmed in oral swabs from two Passeriforms (Pitangus sulphuratus and Gnorimopsar chopi) and a cloacal swab of an unidentified Cathatiform. In conclusion, these findings underscore that birds can participate actively in the epidemiology of C. burnetii, and the presence of bacterial DNA in swabs suggests that wild birds may contribute to environmental dissemination and, due to their high mobility and migratory patterns, may contribute to the long-distance environmental dissemination of C. burnetii, potentially infecting wild and domestic animals as well as human populations.