Microwave energy has been proposed as an alternative to radiofrequency energy for use during catheter ablation procedures. The purpose of this study was to prospectively compare, in an animal model, the lesion size associated with temperature guided catheter ablation using either microwave or radiofrequency energy. Eleven swine underwent catheter ablation with either radiofrequency (N = 4) or microwave energy (N = 7). In each animal catheter ablation was performed at 7-15 sites. At each site energy was delivered for 60 seconds using closed loop feedback temperature control to achieve a target temperature of 70 degrees C. Cardiac catheterization was performed before and after ablation. Animals were sacrificed approximately one month following the ablation procedure. Analysis of lesion size demonstrated that overall lesions created using radiofrequency energy were larger than those created using microwave energy. In the ventricle, lesions created using microwave energy were longer, but had a similar width and depth as those created using radiofrequency energy. An important relation was observed between the depth of lesions created using microwave energy and catheter stability, as evidenced by the temperature profile. Overall, lesions created using microwave energy are smaller than those created using radiofrequency energy. Catheter stability has an important impact on lesion size.