Ablation methods and instruments are disclosed for creating lesions in tissue, especially cardiac tissue for treatment of arrhythmias and the like. Percutaneous ablation instruments in the form of coaxial catheter bodies are disclosed having at least one central lumen therein and having one or more balloon structures at the distal end region of the instrument. The instruments include an energy emitting element which is independently positionable within the lumen of the instrument and adapted to project radiant energy through a transmissive region of a projection balloon to a target tissue site to form a series of lesions on the target tissue.