Embryologic development of atrial septum primum antedates formation of the atrioventricular and semilunar valves. Leftward displacement of the superior attachment of septum primum (LDSP) has only been described in hypoplastic left heart syndrome (HLHS). This study reports the frequency of LDSP in HLHS and correlates LDSP with other echocardiographic features of HLHS. Preoperative echocardiograms for 72 consecutive patients with classic HLHS from 1996 to 2002 at Children's Hospital of Wisconsin were reviewed. One patient was excluded for inadequate imaging. Data for the 71 patients included the following: size, location, and Doppler gradient across the atrial septal defect (ASD); location of attachment of septum primum; size and patency of the aortic valve (AoV) annulus; size and patency of the mitral valve (MV) annulus; ascending aorta diameter (AAD); and left-ventricular end diastolic dimension (LVEDD). Patients were categorized into three groups: aortic atresia/mitral atresia (AA/MA), aortic atresia/mitral stenosis (AA/MS), and aortic stenosis/mitral stenosis (AS/MS). LDSP was seen in 46 of 71 patients (64 %). By diagnostic group, 32 of 35 patients with AA/MA had LDSP (91 %) compared with 10 of 19 AA/MS patients (53 %) and 4 of 17 AS/MS patients (24 %), p < 0.05. AoV patency was seen in 4 of 46 (9 %) patients with LDSP compared with 13 of 25 (52 %) patients with normal atrial attachment, p < 0.005. Mean left heart dimensions in infants with LDSP compared with normal attachment were as follows: AoV annulus 2.24 versus 3.83 mm, AAD 2.34 versus 4.1 mm, MV annulus 3.21 versus 6.48 mm, and LVEDD 6.38 versus 13.83 mm. By two-way analysis of variance of diagnostic category versus atrial septal attachment with interaction, MV annulus and AAD were independently predicted smaller by LDSP versus normal atrial attachment, p < 0.05. Nonsignificant factors included AoV annulus, LVEDD, ASD size, and Doppler gradient. LDSP correlates with more severe maldevelopment of the left heart in patients with HLHS. Because formation of septum primum precedes development and growth of the intracardiac valves, we speculate that LDSP may be an initiating event in the development of HLHS. In addition, prenatal identification of LDSP may help direct planning of potential in utero therapies.