Free-living wild birds are important as reservoirs of Chlamydophila psittaci. Both diseased birds and sub-clinically infected birds can shed chlamydiae and are therefore a potential threat to both human and animal health. Despite its importance for wild birds, poultry, animals and humans, there has not been a study to investigate chlamydiae in wild birds in Egypt. The present study aimed to compare the results of PCR, direct fluorescein conjugated monoclonal antibody staining (FA), Giemsa stain and Gimenez staining as well as serodiagnostic studies on sera by complement fixation test (CFT) in detecting Chlamydophila psittaci in Bubulcus ibis and Upupa epops in Egypt in order to evaluate zoonotic risks for workers that come into contact with these free living birds. Out of 56 Upupa epops (Hoopoe) were investigated, the numbers of positive samples were 53 (94.6%), 44 (78.5%) and 49(87.5%) according to PCR, FA, and mGS, respectively. Out of 52 Bubulcus ibis were investigated, the numbers of positive samples were 48(92.3%), 40(76.9%) and 44(84.6%) according to PCR, FA, and mGS, respectively.