Birds of prey are often affected with external ocular injuries that are routinely treated with antimicrobial agents used for small animals. The resident ocular bacterial and fungal flora is still unknown in birds of prey and this knowledge would be very useful in assessing the accuracy of treatments. In a study involving 65 raptors with healthy eyes, swabs were taken from both eyes to identify the resident bacterial and fungal flora. Fifty-five birds had a positive culture in one or both eyes. Both gram-positive and gram-negative organisms were isolated, with a predominance of Staphylococcus spp., which were found in 52.3% of cultures. Only two fungal species, Aspergillus spp. and Cladosporium spp. were found. The overall results of this study are similar to previous studies carried out in humans and other animals.