Hypoplastic left heart syndrome (HLHS) is a severe form of congenital heart disease characterized by underdevelopment of the left heart. There has been no previously defined “classic” ECG pattern in a large homogenous population of patients with HLHS. We performed a retrospective review of ECGs from neonates with HLHS from 2001 to 2011 with electrocardiograms available prior to surgical intervention. Eighty-nine neonates met the inclusion criteria and were compared to a control population. HLHS patients had a longer PR interval 108 ± 18 versus 98 ± 11 ms (p < 0.05), a wider QRS complex 84 ± 17 versus 54 ± 5 ms (p < 0.05), lower voltage S waves in V1 2.0 ± 3.3 versus 5.8 ± 4.6 mm (p < 0.001) or absent S waves in V1 52 versus 4 % (p < 0.001) and lower voltage R waves in V6 7.8 ± 4.8 versus 9.3 ± 4.2 mm (p < 0.05). Patients with HLHS were more likely to have absent Q waves in the lateral precordial leads 78 versus 0 % (p < 0.001) and inferior leads 20 versus 1 % (p < 0.001) and an abnormal frontal plane QRS axis 26 versus 11 % (p < 0.05). HLHS patients were more likely to have a preexcited appearance 11 versus 0 % (p = 0.001). Despite these findings, 20 % of patients with HLHS had a normal ECG. Compared to age-matched controls, patients with HLHS were more likely to exhibit a longer PR interval, a wider QRS complex, decreased left-sided forces, an absence of septal Q waves in the inferior and lateral leads, an abnormal frontal plane QRS axis and a preexcited appearance.