With stricter laws regulating the capture and possession of wild animals in Costa Rica, local wildlife-rescue centers have been overwhelmed by an influx of confiscated or relinquished illegal pets, specifically of psittacine species. As part of a nationwide health-assessment program targeting these centers, 122 birds representing five psittacine species (Ara macao, Amazona autumnalis, Amazona auropalliata, Amazona farinosa, Aratinga finschi) and one hybrid macaw (Ara macao × Ara ambiguus) were examined and tested between January 2011 and October 2012. Physical examination, hematology, and serum biochemical analyses were performed. Blood and feathers were tested for psittacine beak and feather disease virus (PBFDV) and avian polyomavirus (APV) via PCR. A DNA-based prevalence and sequence analysis characterized the strains of PBFDV and APV isolated. Physical abnormalities observed in 36% of the 122 birds examined were limited to thin body condition and poor feather quality. None of the feather abnormalities were characteristic of disease caused by either PBFDV or APV. Results of hematological and biochemical analyses were within normal limits except for five birds with leukocytosis and heterophilia, three birds with uric acid values above 16 mg/dl, and two additional birds with AST values above 400 IU/L. No hemoparasites were detected during blood smear examination. Overall prevalences of 9.8% (12/122) for PBFDV and 3.3% (4/122) for APV were documented, with only one bird testing positive for both PBFDV and APV. Birds from two of the eight centers were negative for both viruses. Findings from this study constitute the beginning of a standardized surveillance program for Costa Rican rescue centers, targeting the management of avian species enrolled in propagation and reintroduction programs and expanding of the spectrum of pathogen surveillance and husbandry recommendations in prerelease centers.