Abstract Background The QT interval, an electrocardiogram (ECG) parameter, can be corrected for heart rate, giving the QTc. The QTc is an indicator of ventricular repolarisation and is widely used as a predictor of ventricular arrhythmia. Recent studies have reported a relationship between prolonged QTc and atrial fibrillation (AF) development. Purpose We investigated whether a relationship between QTc prolongation and new-onset AF could be identified in the general Japanese population. Methods This retrospective study evaluated the annual health check-up data of 103,304 adults (50,438 males; age, 54±15 years) that did not have AF at baseline, from April 2005 to October 2018. Most participants underwent annual health examinations as recommended by the Japanese health welfare policy. The QTc times were calculated with the Bazett formula (QTc=QT/√RR), using the mean QT and RR intervals. Participants were grouped according to QTc time: long-QTc group (males, >440 ms; females, >460 ms) and normal-QTc group. AF was diagnosed using a 12-lead surface ECG. Logistic regression analyses were performed to determine the strength of the association between prolonged QTc and new-onset AF. Multivariate analyses were adjusted for clinical variables (age, sex, obesity, hypertension, dyslipidaemia, diabetes, estimated glomerular filtration rate, and habitual drinking). Results The median follow-up time for the total study population was 6 years. During follow-up, 341 (0.3%) new cases of AF were recorded. Univariate analysis revealed a significant increase in new-onset AF in the long-QTc group (odds ratio OR, 2.80; 95% confidence interval CI, 1.85–4.25; p<0.001). After adjusting for clinical variables, multivariate analysis revealed that a long QTc was significantly associated with new-onset AF (OR, 1.71; 95% CI, 1.12–2.61; p=0.013). In the multivariate analysis, age (OR, 1.06; 95% CI, 1.05–1.07; p<0.001), sex (OR, 2.55; 95% CI, 1.95–3.33; p<0.001), obesity (OR, 1.46; 95% CI, 1.16–1.84; p=0.001), and habitual drinking (OR, 1.90; 95% CI, 1.50–2.41; p<0.001) were also significant predictors of new-onset AF. Conclusions Prolonged QTc is associated with an increased risk of new-onset AF in the general Japanese population. The mechanism of this causal relationship requires further investigation.