Subaortic stenosis (SAS) is one of the most common congenital heart diseases (CHD) in dogs with Boxers being predominantly affected. However, the increasing availability of modern diagnostic imaging systems now allows a better assessment of cardiac morphology and function, thereby facilitating early detection of CHD in awake animals. In this context, the case records of Boxer dogs diagnosed with CHD using echocardiography combined with Doppler mode, were retrospectively reviewed (1998–2005). One hundred and five Boxers exhibiting either a single CHD (53/105, 50.5%) or association of several CHD (52/105, 49.5%) were included. The most common CHD was atrial septal defect (ASD) observed in 56.2% of these animals (59/105), followed by mitral dysplasia (58/105, 55.2%), and SAS (49/105, 46.7%). SAS was associated with one or two CHD in 29.5% of cases (31/105). Most of the dogs with a low intensity left heart base systolic murmur had an isolated ASD whereas most of the dogs with a similar but high intensity murmur had SAS, either isolated or associated with a concurrent CHD. The incidence of ASD and mitral dysplasia in Boxer dogs is higher than previously assumed, and ASD is a common cause of left heart base systolic murmur in this breed of dog. This confirms that the detection of such a murmur should not be used as the unique criterion for diagnostic confirmation of SAS.