A 12-week old, entire female Border terrier weighing 3.5 kg was presented for investigation of a continuous left heart base murmur. The clinical presentation and preoperative echocardiogram were consistent with a standard morphology of patent ductus arteriosus (PDA) but a discrete ductal vessel was not identified during surgical dissection. Surgery had to be abandoned due to deterioration of the patient's condition under general anaesthesia which led to cardiorespiratory arrest and death despite attempts at resuscitation. Necropsy identified a recess within the wall of the aorta communicating with the pulmonary artery via an ostium at the heart base which determined this structure as an intramural PDA. This morphology of PDA is previously unreported. This report demonstrates that an intramural PDA is not readily identifiable surgically because of the absence of a discrete ductal vessel and it is important to appreciate that unusual morphologies of PDA may occur.