Arrhythmias (irregular heart beats, such as atrial flutter and atrial fibrillation) may arise as the L-TGA patient ages. These result from surgical modifications of the heart tissue, enlargement of the atria, or from other causes. They are treated with medicines or by radiofrequency ablation (the neutralization of offending conduction pathways) during a cardiac catheterization procedure.

Heart block may also develop with time. This is a condition in which the impulses from the heart's natural pacemaker (the sinoatrial node) are delayed (1st degree heart block), partially blocked (2nd degree), or completely blocked (3rd degree) as they make their way to the pumping chambers (the ventricles). Treatment may involve the insertion of a pacemaker. Sudden death from conduction anomalies in the heart is comparatively rare with L-TGA.