Native and exotic avian species can act as reservoirs of pathogens, including bacteria and viruses, with conservation and public health implications. A retrospective study on the diagnosis and frequency of diseases in wild and exotic avian species was conducted. The occurrence of particular diseases was associated with the type of captivity or the bird’s origin. The investigation included macroscopic and microscopic descriptions and the molecular determination of the causative agent(s). Additional immunohistochemical (IHC) analysis, PCR, and genetic sequencing were conducted. A total of 243 cases were compiled for the study, mainly consisting of native wild species (39.1%) obtained from illegal trade. Primary infectious diseases, mainly parasitic (18.1%) and viral (17.7%), were the most common, although coinfections were substantial (18.1%) in birds rescued from trafficking. Fractures and neoplasms accounted for 3.7% and 3.3% of the cases, respectively. Parasitic and viral diseases were the most common in both exotic and wild birds. Chlamydia psittaci, a lethal and zoonotic bacterium, was an important cause of death, especially in native Psittaciformes. The recent detection of Psittacid alphaherpesvirus 5 (PsAHV 5) in exotic psittacines and the diagnosis of coinfections in trafficked birds highlight the importance of monitoring avian health to control potential pathogens that may endanger conservation efforts.