Background Prolongation of the QT on the surface electrocardiogram can be due to either genetic or acquired causes. Distinguishing congenital long QT syndrome (LQTS) from acquired QT prolongation has important prognostic and management implications. We aimed to investigate if quantitative T‐wave analysis could provide a tool for the physician to differentiate between congenital and acquired QT prolongation. Methods Patients were identified through an institution‐wide computer‐based QT screening system which alerts the physician if the QTc ≥ 500 ms. ECGs were retrospectively analyzed with an automated T‐wave analysis program. Congenital LQTS was compared in a 1:3 ratio to those with an identified acquired etiology for QT prolongation (electrolyte abnormality and/or prescription of known QT prolongation medications). Linear discriminant analysis was performed using 10‐fold cross‐validation to statistically test the selected features. Results The 12‐lead ECG of 38 patients with congenital LQTS and 114 patients with drug‐induced and/or electrolyte‐mediated QT prolongation were analyzed. In lead V5, patients with acquired QT prolongation had a shallower T wave right slope (−2,322 vs. −3,593 mV/s), greater T‐peak‐Tend interval (109 vs. 92 ms), and smaller T wave center of gravity on the x axis (290 ms vs. 310 ms; p < .001). These features could distinguish congenital from acquired causes in 77% of cases (sensitivity 90%, specificity 58%). Conclusion T‐wave morphological analysis on lead V5 of the surface ECG could successfully differentiate congenital from acquired causes of QT prolongation.