Background: In about 20-25% of patients with congenital long QT syndrome (LQTS) a causative pathogenic mutation is not found. The aim of this study was to explore the prevalence of alternative cardiac diagnoses among patients exhibiting prolongation of QT interval with negative genetic testing for LQTS genes. Methods: We conducted a retrospective analysis of 239 consecutive patients who were evaluated in the inherited arrhythmia clinic at the Toronto General Hospital between July 2013 and December 2015 for possible LQTS. A detailed review of the patients' charts, electrocardiograms, and imaging was carried out. Results: The analysis included 56 gene-negative patients and 61 gene-positive patients. Of the gene-negative group, 25% had structural heart disease compared to only 1.6% of gene-positive patients (P < 0.001). Structural heart disease was more likely if only one abnormal QTc parameter was found in the course of the evaluation (35.2% vs 9.1%, P = 0.01). The most common structural cardiac pathology was bileaflet mitral valve prolapse (8.9%). No gene-positive patient had episodes of nonsustained ventricular tachycardia, compared to seven of the gene-negative patients (0% vs 12.5%, P = 0.005). Conclusions: Structural pathology was detected in a quarter of gene-negative patients evaluated for possible LQTS. Hence, cardiac imaging and Holter monitoring should be strongly encouraged to rule out structural heart disease in this population.