Abstract Introduction Drug-induced long QT syndrome (DI-LQTS) is a clinical entity with a poorly defined etiopathogenesis. Purpose The objective of the study was to determine the genetic basis of a prospective cohort of patients with DI-LQTS in the setting of a tertiary hospital center. Methods Prospective observational study with consecutive inclusion of patients with the diagnosis of DI-LQTS according to standard criteria, in a tertiary hospital, between 2018 and 2022. A genetic study was performed through massive DNA sequencing to identify variants in known genes associated with cardiopathy, arrhythmogenic and cardiomyopathy. Results 86 patients (age 65±15 years, 59% men) were included. The mean corrected QT interval (QTc) of the entire cohort was 543±56 ms. The drugs associated with QTc interval prolongation were: psychotropics 51%, antiarrhythmics 38%, anesthetics 30%, antibiotics 16%, antineoplastics 5%, others 4%. Twenty-one patients (24%) presented with ventricular arrhythmias at the time of drug-induced QTc prolongation: 10 (12%) ventricular fibrillation, 7 (8%) sustained ventricular tachycardia, 3 (3%) non-sustained ventricular tachycardia, 1 (1%) frequent ventricular premature beats. Genetic information was obtained in 83 (97%) patients. 17 pathogenic mutations associated with heart disease were identified in 15 (18%) patients: 4 (5%) patients with 5 mutations in ion channel genes (KCNE1, KCNE1B, KCNH2, RYR1, RYR2), and 12 (14%) patients with 12 mutations in genes associated with cardiomyopathy (NF1, PKD2, ABCC6, TTN, FHOD3, MYO6, COL11A1, CCDC40, CRELD1, COL4A1). Two patients had 2 pathogenic mutations each, one of them with both mutations associated with channelopathy, and another with a mutation associated with channelopathy and a second mutation related to cardiomyopathy. Only 1 patient carrying a pathogenic mutation related to cardiomyopathy had a clear phenotype, while in 3 carrier patients there was a history of transient systolic dysfunction, 2 due to tachycardiocardiopathy and 1 due to peripartum cardiomyopathy. The identification of a pathogenic mutation was not related to significant differences in QTc interval prolongation (544±63 vs 542±55 ms) or risk of ventricular arrhythmias (26% vs 24%). Conclusions The genetic basis of drug-induced long QT syndrome is essentially different from that of the congenital form of the disease. The identification of pathogenic mutations in genes associated with cardiomyopathy is relatively frequent, while those associated with ion channel genes are uncommon.