Atrial fibrillation (AF) appears in the presence or absence of structural heart disease. The majority of foci causing AF are located near the ostia of pulmonary veins (PVs), where cardiomyocytes and vascular smooth muscle cells interdigitate. Connexins (Cx) form gap junction channels and participate in action potential propagation. Genetic variants in genes encoding Cx40 and Cx37 affect their expression or function and may contribute to PV arrhythmogenicity. DNA was obtained from 196 patients with drug-resistant, symptomatic AF with and without structural heart disease, who were referred for percutaneous catheter ablation. Eighty-nine controls were matched for age, gender, hypertension, and BMI. Genotyping of the Cx40 -44G>A, Cx40 +71A>G, Cx40 -26A>G, and Cx371019C>Tpolymorphisms was performed. The promoter A Cx40 polymorphisms (-44G>Aand +71A>G) showed no association with non-structural or structural AF. Distribution of the Cx40 promoter B polymorphism (-26A>G) was different in structural AF when compared to controls (p= 0.03). There was no significant difference with non-structural AF (p= 0.50). The distribution of the Cx371019C>Tpolymorphism was different in non-structural AF (p= 0.03) but not in structural AF (p= 0.08) when compared to controls. Our study describes for the first time an association of drug-resistant non-structural heart disease AF with the Cx371019C>Tgene polymorphism. We also confirmed the association of the Cx40 -26G>Apolymorphism in patients with AF and structural disease.