New transvenous devices using cryoenergy have been recently introduced to perform pulmonary vein isolation (PVI) for the treatment of atrial fibrillation (AF). Experimental data suggested that cryoenergy (CRYO) produced less endothelial disruption and platelet activation than radiofrequency energy (RF) offering safety benefits. We aimed to compare both systems with regards to safety in patients by measuring for the first time sensitive laboratory markers of cell damage. platelet activation and inflammation after a PVI using either one of those energies. Sixty patients with symptomatic drug-resistant AF referred for PVI (56 ± 9 years of age, 48 males. 38 with paroxysmal and 22 with persistent AF) were randomly assigned to undergo the ablation procedure using either an open irrigated tip RF catheter (Thermocool®. Biosense Webster) or a cryoballoon catheter (Arctic front®. Medtronic). Systemic markers of cell damage (procoagulant microparticles MPs of various cellular origin, troponin T, CK and CK-MB). platelet activation (ADP-induced light transmittance aggregation LTA, expression of the platelet surface proteins P-selectin pSEL and activated GPIIb/IIIa PAC-1) and inflammatory response (hs-CRP) were determined frequently before and 4, 24 and 48 hours after the procedure. Procedure time was significantly shorter in patients treated with the cryoballoon (177 ± 30 min versus 200 ± 46 min. p = 0.028), but there were no differences in fluoroscopic time, clinical event rate and success rate. Post-procedural increases of MPs Troponin T and hs-CRP were observed but there were no consistent differences in parameters used for comparative laboratory safety assessment of the ablation systems using either cryoenergy or radiofrequency energy. Neither systematic sensitive markers of cell damage, of platelet activation nor of inflammatory response could detect any difference in the safety profile between cryoenergy and RF energy used for transseptal PVI in patients with AF.