Purpose Endothelial dysfunction plays a major role in erectile dysfunction (ED). Atrial fibrillation (AF), regardless of subtype, is associated with a prothrombotic state, which is related to endothelial dysfunction. In this study, we aimed to determine whether AF is an independent risk factor for ED. Methods A total of 50 patients diagnosed with paroxysmal lone AF and 80 age-, gender-, and body mass indexmatched controls without AF who admitted to outpatient clinics at a tertiary center were enrolled. Diagnosis of ED was performed by using Sexual Health Inventory for Men (SHIM) questionnaire. Patients with a SHIM score <= 21 were defined as having ED. Results Mean age of patients were 51.8 +/- 7.7 and all of the study population were male. Twenty-nine of 50 patients in lone AF group and 25 of 80 patients in control group were diagnosed with ED (58 vs 31.2 %, p = 0.002). Mean SHIM score was significantly lower in lone AF group compared with controls (20.74 +/- 2.67 vs 22.39 +/- 2.21, p< 0.001). The multivariate stepwise logistic regression analyses showed that lone AF (OR 1.94 (1.44-2.46), p < 0.001), smoking (OR 1.92 (1.35-2.44), p = 0.003), fasting blood glucose (OR 1.51 (1.10-1.85), p = 0.012), and uric acid levels (OR 1.56 (1.131.92), p = 0.009) were independent predictors of ED. Conclusions Beat-to-beat variation may lead to ED in patients with paroxysmal lone AF and questioning erectile function in patients with lone AF may be recommended.