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Abstract Background A normal visceral arrangement is called situs solitus, whereas a state of visceral arrangement in a mirror-like positional relationship is called situs inversus (SI). Among the SI, the state in which the positions of only some thoracoabdominal organs are reversed is called situs inversus partialis, and the state in which the positions of all thoracoabdominal organs are reversed is called situs inversus totalis (SIT). Clinical information on dogs with SIT is limited. Case presentation A 4-month-old Shiba Inu was referred with depression and neurological symptoms as the chief complaints. Computed tomography (CT) revealed the patient had SIT with an extrahepatic portosystemic shunt (EHPSS) and azygos continuation of the caudal vena cava. In addition, complete reversal of the lung lobes and cardiovascular system in the thoracic cavity was confirmed. The patient underwent surgery for partial attenuation of the EHPSS on day 8 after the initial examination. On day 124, after the initial examination, a second surgery was performed for complete attenuation. Under celiotomy, the positions of all abdominal organs, except for the rectum, were inverted; thus, SIT was confirmed via gross observation. In addition, the use of braided nylon sutures partially attenuated the concurrent portocaval shunt. At the conclusion of this study, approximately 6 years had passed since the second surgery, and the patient had a good general condition without any medications. Conclusion In SIT, the complex anatomy of the abdominal organs and vessels is difficult to identify via gross observation. In contrast, CT is effective in detecting vascular abnormalities, confirming the anatomical position of each organ, and allowing for the definitive diagnosis of SIT.