Background: Congenital long QT syndrome(LQTS) is a genetic disease that brings prolongation of the QT interval on an electrocardiogram and leads to syncope and sudden death by a fatal ventricular arrhythmia. In Korea, there are studies about the clinical characteristics and treatment of LQTS but none on the molecular biological evaluation of its genetic mutation. Methods: Six nationwide university hospitals segregated DNA from the blood of 10 patients with diagnosed LQTS to analyze genetic mutation. Results: Nine out of ten individuals were female. Eight showed genetic mutation. Three had an abnormality in the KvLQT1, 6 in the HERG and 2 had abnormalities in both KvLQT1 and HERG. None had abnormalities in KCNE1 and 2 showed no abnormalities in KvLQT1, HERG or KCNE1. Conclusion: Congenital LQTS shows various genetic mutations indicating the necessity for further organized study in more individuals for confirmation of the relationship between the two.