Multidetector computed tomography (MDCT) scans were performed in clinically healthy, nonanesthetized, standing little penguins (Eudyptula minor) to determine reference ranges for air-sac and lung volumes, as well as lung density. Five of 15 clinically healthy birds were diagnosed with pulmonary granulomas on initial MDCT scans. Granulomas were not readily apparent on radiographs, even in cases where the entire normal pulmonary parenchymal architecture was effaced on the MDCT scan. Serial MDCT scans after antifungal and antimycobacterial therapies demonstrated a response to treatment. MDCT scanning in nonanesthetized little penguins proved to be a well-tolerated, non-invasive imaging modality for respiratory diseases that are otherwise difficult to diagnose, including aspergillosis and mycobacteriosis.