Background Though spontaneous closure of isolated congenital ventricular septal defects in humans is very common, it has been rarely reported in dogs. Case presentation A 4 month old Havanese dog and a 4.5 month old Chihuahua x Jack Russell terrier cross were presented for murmur evaluation to the authors’ institution. Both puppies were clinically healthy and had a loud systolic murmur on the right hemithorax. Echocardiography in both dogs revealed a small, isolated, restrictive perimembranous congenital ventricular septal defect. No echocardiographic signs of left ventricular volume overload or pulmonary hypertension were present. Re-check auscultation in both dogs revealed the absence of a murmur, and echocardiography showed no flow through the interventricular septum. In the 9 kg Havanese dog and the 4 kg mixed breed dog, spontaneous closure occurred at 13–17 months and 12–30 months, respectively. Conclusions In both dogs the spontaneous closure of a congenital perimembranous ventricular septal defect took place in a young adult age. The mechanism of closure remains unclear.