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Introduction: Prospective studies on rivaroxaban and apixaban have shown the safety and efficacy of direct anticoagulation agents (DOAC)s used peri-procedurally during radiofrequency ablation (RFA) of atrial fibrillation (AF). Studies comparing the two agents have not been performed. Methods: Consecutive patients from a prospective registry who underwent RFA of AF between April 2012 and March 2015 and were on apixaban or rivaroxaban were studied. Clinical variables and outcomes were noted. Results: There were a total of 358 patients (n = 56 on apixaban and n = 302 on rivaroxaban). There were no differences in baseline characteristics between both groups. The last dose of rivaroxaban was administered the night before the procedure in 96% of patients. In patients on apixaban, 48% of patients whose procedure was in the afternoon took the medication on the morning of the procedure. TIA/CVA occurred in 2 patients (0.6%) in rivaroxaban group with none in apixaban group (p = 0.4). There was no difference in the rate of pericardial effusion between apixaban and rivaroxaban groups [1.7% vs 0.6% (p = 0.4)]. Five percent of patients in both groups had groin complications (p = 0.9). In apixaban group, all groin complications were small hematomas except one patient who had a pseudoaneurysm (1.6%). One pseudo-aneurysm, 1 fistula and 3 large hematomas were noted in patients on rivaroxaban (1.7%) with the rest being small hematomas. DOACs were restarted post procedure typically 4 h post hemostasis. Conclusions: Peri-procedural uninterrupted use of apixaban and rivaroxaban during AF RFA is safe and there are no major differences between both groups.