Atrial septal aneurysm (ASA) is a saccular deformity located in the atrial septum. Atrial arrhythmias are common in patients with ASA. Atrial electromechanical delay (AEMD) can be used to evaluate development of atrial arrhythmias in various settings. The aim of the study was to investigate the relationship between ASA, cardiac arrhythmias and AEMD. Seventy patients with ASA served as the study group (30 men; mean age, 33.6 ± 10.9 years) and 70 healthy volunteers served as the control group (34 men; mean age, 31.4 ± 7.8 years). ASAs were diagnosed by transthoracic echocardiography based on the criteria of a minimal aneurysmal base of ≥ 15 mm; and an excursion of ≥ 10 mm. Inter-AEMD and intra-AEMDs of both atrium were measured from parameters of tissue Doppler imaging. There was no significant difference between the study and control groups in terms of age, gender, left atrium diameter, and left ventricular ejection fraction. Inter-AEMD (50.7 ± 22.5 ms vs. 36.9 ± 12.0 ms) and intra-left AEMD (44.6 ± 17.4 ms vs. 30.7 ± 11.6 ms) were significantly higher in patients with ASA with respect to control group. Inter-AEMD (63.6 ± 20.1 ms vs. 45.1 ± 21.5 ms, P = 0.001), intra-left AEMD (55.3 ± 15.6 ms vs. 40.1 ± 16.2 ms, P = 0.001), diameter of the ASA (19.9 ± 3.6 mm vs. 17.1 ± 2.7 mm, P = 0.001) and P wave dispersion (18.5 ± 6.7 ms vs. 11.8 ± 7.3 ms, P = 0.001) were significantly greater in the subgroup with arrhythmias compared to the subgroup without arrhythmias. Inter-AEMD and intra-left AEMD were found to be significantly prolonged in patients with ASA. Being a non-invasive, inexpensive and simple technique AEMD may provide significant contributions to assess the risk for paroxysmal supraventricular arrhythmia in patients with ASA.