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Background The domestic chinchilla has been descended from Chinchilla lanigera (long-tailed Chinchilla) or Chinchilla chinchilla (short-tailed Chinchilla). Both species of chinchilla are currently listed as endangered by the IUCN Red List of Threatened Species. Over the past 20 years, they have spread as pets and overall knowledge about their care is improving. The present case report describes a congenital diaphragmatic hernia in a Chinchilla lanigera. Case presentation A 1-year-old, 420 g female chinchilla (Chinchilla lanigera) was presented for clinical examination due to 2 days haematuria episodes and anorexia. A complete haematological analysis was performed, showing a moderate neutrophilia and severe renal involvement. X-rays showed severe intestinal meteorism affecting mostly the cecum, and a soft tissue density mass with translucent areas located in the caudal thorax, making it hard to distinguish the cardiac silhouette. A barium swallow (barium sulfate) was performed and after 20 min, radiograms were performed again, showing part of the stomach dislocated in thorax. Ultrasound was also carried out, confirming the partial stomach herniation into the thoracic cavity and a severe nephropathy. The patient was euthanized according to the owner’s wish and a complete necropsy was performed. The diagnosis was congenital diaphragmatic hernia concomitant to a severe bilateral bacterial glomerulonephritis. Discussion and conclusions Diaphragmatic hernias can be either congenital or acquired. About CDHs in pet chinchillas, literature is still lacking. In this patient there was no history of previous traumas. No scar tissue or thickening involved margins of the pathological diaphragm window at the necropsy, supporting the hypothesis of a congenital defect. Glomerulonephritis most often results from immune-mediated mechanisms, generally after the deposition of soluble immune complexes within the glomeruli. This mechanism is favoured by a prolonged antigenemia that could occur during specific viral infections, chronic bacterial infections, chronic parasitism, autoimmune diseases and neoplasia. Few cases of nephritis are described in chinchillas (Chinchilla lanigera), mostly related to bacterial sepsis or less commonly involving fungi. The evidence of bacterial aggregates in kidneys at the histopathology, confirmed the infective aetiology. No relationship between the diaphragmatic hernia and glomerulonephritis was found in this report.