The development of the heart is a complex process during which different cell types progressively contribute to shape a four-chambered pumping organ. Over the last decades, our understanding of the specification and transcriptional regulation of cardiac development has been greatly augmented as has our understanding of the functional bases of cardiac electrophysiology during embryogenesis. The nascent heart gradually acquires distinct cellular and functional characteristics, such as the formation of contractile structures, the development of conductive capabilities, and soon thereafter the co-ordinated conduction of the electrical impulse, in order to fulfil its functional properties. Over the last decade, we have learnt about the consequences of impairing cardiac morphogenesis, which in many cases leads to congenital heart defects; however, we are not yet aware of the consequences of impairing electrical function during cardiogenesis. The most prevalent cardiac arrhythmia is atrial fibrillation (AF), although its genetic aetiology remains rather elusive. Recent genome-wide association studies have identified several genetic variants highly associated with AF. Among them are genetic variants located on chromosome 4q25 adjacent to PITX2, a transcription factor known to play a critical role in left-right asymmetry and cardiogenesis. Here, we review new insights into the cellular and molecular links between PITX2 and AF.