Introduction: Congenital long QT syndrome (LQTS) is a cardiac disorder characterized by QT interval prolongation at basal ECG. Different LQTS genes encode ion channel subunits or proteins involved in regulating cardiac ionic currents. Long QT syndrome type 6 (LQT6) is caused by mutation in the KCNE2 gene. Our research aimed to analyze genetic variants of KCNE2 gene causing the disease in Iranian population. Methods: Twenty nine patients consented for participation in the study. They were diagnosed based on Schwartz's criteria. After DNA extraction from peripheral blood cells, two exons of the KCNE2 gene were amplified. Afterwards, PCR-SSCP was carried out for screening the possible mutated gene variants. As the last verification step, direct sequencing was done to determine the sequence. Results: All samples were detected by PCR-SSCP and sequenced. None of the patients had the mutation in the KCNE2 gene. Conclusion: Investigating a genetic variant associated with LQTS, in Iranian patients clinically diagnosed with LQT6, no association was found between the disease and KCNE2 gene. Other previously identified genes, especially the major genes, should be considered for further investigation.