Summary. Background: The risk factors associated with, and the incidence of systemic embolism in patients with atrial fibrillation (AF) are poorly understood. Objectives: We studied the association between AF and upper limb thromboembolectomy involving brachial, ulnar or radial artery in a national cohort study that included all individuals aged 40–99 years with incident AF. Methods: Data were retrieved from the Danish National Vascular Registry, the National Registry of Patients, the Danish Civil Registration System and Statistics Denmark. Results: In total, 131 476 patients (68 042 men and 63 434 women) with AF without previous thromboembolectomy in the upper limb were registered. In the study cohort, 130 men underwent upper limb thromboembolectomy over 220 890 person-years of observation, whilst 275 women underwent thromboembolectomy over 197 777 patient-years. The incidence per 100 000 person-years was 58.9 (95% CI, 49.2–69.8) for men and 139.1 (95% CI, 123.1–156.5) for women. The relative risk of thromboembolectomy among patients with AF compared to the background population was 7.5 (95% CI, 6.3–8.9) for men, and 9.3 (95% CI, 8.3–10.5) for women. Women with AF had a relative thromboembolectomy risk of 1.8 (95% CI, 1.5–2.3) compared to men with AF. Among patients with AF, history of hypertension (HR 2.2–2.9), myocardial infarction (HR 2.9–3.9), heart failure (HR 1.6–1.9) and stroke (HR 2.2–3.8) were significantly associated with increased risk of thromboembolectomy in both men and women. Conclusions: AF substantially increases the risk of upper limb thromboembolectomy. This risk is higher with increasing age, female gender, and associated with hypertension, myocardial infarction, heart failure and stroke.