Five variations of atrial septal morphology occur in hypoplastic left heart syndrome. One variety, termed anomalous attachment of septum primum, has been described only in necropsy series. Two-dimensional echocardiography was utilized to determine the incidence of this anomaly in patients with left atrioventricular (AV) valve underdevelopment, including those with other ventriculoarterial alignments, such as transposition of the great arteries. Forty-eight (37%) of 129 patients with normally aligned great arteries (and two ventricles) had anomalous attachment of septum primum. Ten (34%) of 29 patients with double outlet right ventricle and left AV valve underdevelopment had this anomaly. Four (50%) of eight patients with single ventricle exhibited this atrial septal variant. The most reliable view to identify anomalous attachment was the subcostal left oblique-equivalent cut. Recognition of atrial septal morphology has implications for preoperative and intraoperative management of patients with left AV valve underdevelopment. The similar prevalence of this atrial septal variant in patients with normally aligned great arteries, double outlet right ventricle and transposed great arteries suggests that there may be a common mechanism for left AV valve underdevelopment that is independent of the development of the arterial portion of the heart.