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In acute pulmonary thromboembolism (PTE), right ventricular pressure overload impairs right-sided cardiac conduction and repolarization. We hypothesized that if heterogeneity of repolarization between right and left ventricles occurs in acute PTE, there would be the difference of repolarization between them. Therefore, we aimed to evaluate the diagnostic value of corrected QT interval (QTc) difference between leads V1 and V6 (V1 − V6) in patients with acute PTE.A total of 89 patients with suspected acute PTE who underwent computed tomographic angiography (CTA) were enrolled from January to December 2015. PTE was identified by CTA. We compared electrocardiographic (ECG) parameters, especially QTc difference (V1 − V6) between patients with PTE and those without PTE.Acute PTE was finally diagnosed in 45 patients. Clinical situations including the chief complaint were not different between PTE and non-PTE groups. S1Q3T3, a traditional ECG marker, had no diagnostic value for acute PTE. Patients with PTE had a significantly longer mean QTc in V1 (454.6 ± 44.3 vs 417.5 ± 31.3 ms, P < .001) and larger QTc difference (V1 − V6) (34.8 ± 30.5 vs –12.5 ± 16.6 ms, P < .001) than non-PTE controls. QTc difference (V1 − V6) was negative in all patients without PTE. PTE patients had a higher prevalence of T wave inversion in leads III (51.1% vs 29.5%, P = .038) and V1 (82.2% vs 38.6%, P < .001). A QTc difference (V1 − V6) of ≥20 ms identified PTE with 82.2% sensitivity, 100.0% specificity, and 100.0% positive predictive value.QTc difference (V1 − V6) had an excellent diagnostic value for differentiating patients with and without acute PTE.