Atrial fibrillation is associated with the activation of inflammatory processes [e.g. higher concentrations of pro-inflammatory cytokines interleukin-6 (IL-6), C-reactive protein (CRP)], as well as a pro-thrombotic state [e.g. increased concentration of serum pro-thrombotic markers P-selectin and CD40 ligand (CD40L)]. The aim of the present study was to establish, whether successful epicardial ablation of AF leads to decreased concentrations of traditional inflammatory and thrombotic markers. Twenty-five patients with symptomatic paroxysmal or persistent AF were prospectively studied. All underwent epicardial isolation of pulmonary veins. The success of the ablation was assessed clinically and with three Holter recordings. Blood samples were drawn before, three and six months after surgery. Serum concentrations of IL-6, interleukin-10 (IL-10), CRP, CD40L and P-selectin were measured using ELISA. AF was successfully ablated in 15 patients (SR group). In the other 10 patients (AF group), AF re-occurred during follow-up. Neither group differed with respect to age, gender, left ventricular ejection fraction, or preoperative concentrations of measured molecules. The concentrations of IL-6, CRP and CD40L decreased in successfully ablated patients; however, there was no change in the concentrations of these molecules in the AF group. The concentrations of IL-10 and P-selectin were unchanged in both groups during follow-up. Successful ablation of AF, with sinus rhythm restoration and maintenance, is associated with decreased serum levels of markers of inflammation.