Abstract Background Complete transposition of the great arteries is a congenital cardiac malformation occasionally encountered in cattle and other species. The objective of the present report was to provide a detailed clinical, echocardiographic and post mortem description of a calf presenting with this condition. Case presentation A 6-week old male Belgian Blue cross-breed calf was examined for respiratory distress and exercise intolerance. The patient was bright, alert and responsive without any neurologic abnormalities but was exercise intolerant, had marked cyanosis, tachycardia, tachypnea, a pansystolic heart murmur as well as a bilaterally palpable thrill over the heart. Arterial blood gas analysis revealed marked hypoxemia (PaO 2 = 23 mmHg, O 2 sat = 41.1%), mild hypercapnia and compensated respiratory acidosis. Echocardiographic examination revealed a complete transposition of the great arteries in combination with a ventricular septal defect through which blood shunted bidirectionally. Cardiac catheterization confirmed that arterialization of blood of the systemic circulation solely occurred in the right ventricle through blood shunting from the left into the right ventricle. Results of post mortem examination are presented. Conclusion Complete transposition of the great arteries is a cyanotic congenital anomaly repeatedly reported in calves that should be considered as differential diagnosis in patients presenting with hypoxemia more severe than commonly encountered with other congenital cyanotic heart conditions. We give a comprehensive summary of the clinical presentation, diagnostic work-up and post mortem examination of a Belgian Blue cross-breed calf with complete transposition of the great arteries