Atrial septal aneurysm is a rare malformation that may occur as an isolated abnormality or in association with various cardiac defects or with connective tissue disease. The reported incidence in adults is 0.2% and in children 4.9% which suggests spontaneous regression with advancing age. Atrial septal aneurysm may be complicated by thromboembolism, valvular obstruction or arrhythmias. Supraventricular arrhythmias have been reported in as much as 16% of the cases, most commonly paroxysmal supraventricular tachycardia, supraventricular extrasystoles and atrial flutter. The relationship between the arrhythmias and the atrial septal aneurysm is still controversial. Two cases of atrial septal aneurysm in neonates are described, who presented with arrhythmias: supraventricular extrasystoles with aberrant conduction and atrial flutter with variable conduction, respectively. One of them required treatment with various anti-arrhythmia agents. During follow-up the arrhythmias remitted with spontaneous involution of the aneurysm. In the presence of the supraventricular arrhythmias in neonates, atrial septal aneurysm needs to be ruled out as a potential cause.