Markers of myocardial injury and inflammation have been shown to be elevated following radiofrequency (RF) ablation. This study aimed to compare RF ablation and cryoablation for their impact on markers for myocardial injury and inflammation. Nineteen patients received catheter ablation for atrial flutter by either cryoablation (10 patients) or open-irrigated RF ablation (nine patients). Venous blood samples for troponin T (TnT), creatinkinase (CK), and the cardiac isoenzyme MB (CKMB) were obtained before, at six hours after the end of ablation, and the following day. C-reactive protein (CRP) levels were measured before ablation and the following day. Bidirectional isthmus block was achieved in all patients. Cryoablation showed significantly higher TnT following ablation (0.85 microg/l +/- 0.39 microg/l) compared to RF ablation (0.36 microg/l +/- 0.24 microg/l; p= 0.01) with declining levels the following day (cryoablation: 0.58 microg/l +/- 0.20 microg/l; RF ablation 0.34 microg/l +/- 0.21 microg/l; p= 0.03). We observed equal findings for CK and CKMB, both significantly higher in cryoablation. RF ablation led to a nonsignificant rise in CK and CKMB. CRP was elevated significantly higher following RF ablation (12.3 mg/dl +/- 4.1 mg/dl) compared to cryoablation (6.9 mg/dl +/- 4.0 mg/dl; p= 0.01). We show reduced inflammation despite higher markers for myocardial injury in cryoablation. The difference in biomarkers reflects different lesion formation in cryoablation and RF ablation. Cryoablation shows less systemic inflammatory reaction. This might be due to less endothelial damage and surface thrombosis in cryoablation.