A 3-day-old alpaca cria presented for progressive weakness and dyspnea since birth. Complete bloodwork, thoracic radiographs, and endoscopic examination of the nasal passages and distal trachea revealed no significant findings. Echocardiogram and contrast study revealed a single artery overriding a large ventricular septal defect (VSD). A small atrial septal defect or patent foramen ovale was also noted. Color flow Doppler and an agitated saline contrast study revealed bidirectional but primarily right to left flow through the VSD and bidirectional shunting through the atrial defect. Differential diagnosis based on echocardiographic findings included common arterial trunk, Tetralogy of Fallot, and pulmonary atresia with a VSD. Postmortem examination revealed a large common arterial trunk with a quadricuspid valve overriding a VSD. Additionally, defect in the atrial septum was determined to be a patent foramen ovale. A single pulmonary trunk arose from the common arterial trunk and bifurcated to the left and right pulmonary artery, consistent with a Collet and Edwards' type I common arterial trunk with aortic predominance. Although uncommon, congenital cardiac defects should be considered in animals presenting with clinical signs of hypoxemia, dyspnea, or failure to thrive.