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The anatomy of the avian gastrointestinal (GI) tract is unique and significantly different from that of other animals. The characteristics of the avian GI tract allow the different species to adapt and thrive in their habitats. Infectious diseases of bacterial, viral, fungal, and parasitic origin commonly affect avian species. The significance and the nature of these pathologies vary with species and if they live in the wild or a captive environment. This review compiles information available in the literature on specific infectious processes that were considered relevant and clinically significant by the authors. Clinicians should be knowledgeable and aware of the infectious agents, clinical signs associated with disease, diagnostic techniques, and treatment methodologies currently available regarding diseases that affect the avian GI tract. Recent information that provides new insight to these infectious processes is the focus of this article.