Introduction Atrial refractoriness may be an important determinant of atrial fibrillation (AF) risk, but its measurement is not clinically accessible. Because the QT interval predicts incident AF and the atrium and ventricle share repolarizing ion currents, we investigated the association between an individual’s QT interval and atrial effective refractory period (AERP). Methods In paroxysmal AF patients presenting for catheter ablation, the QT interval was measured from the surface 12-lead ECG. The AERP was defined as the longest S1-S2 coupling interval without atrial capture using a 600 ms drive cycle length. Results In 28 patients, there was a positive correlation between QTC and mean AERP. After multivariate adjustment, a 1 ms increase in QTC predicted a 0.70 ms increase in AERP. Conclusions The QTc interval reflects the AERP, suggesting that the QTc interval may be used as a marker of atrial refractoriness relevant to assessing AF risk and mechanism-specific therapeutic strategies.