An esophageal ablation system including a positioner, an elongated, flexible shaft extending from the positioner, and a microwave emitter assembly disposed near the distal end of the shaft. The emitter assembly includes one or more microwave antennae and a balloon for spacing the antennae relative to target tissue. The device may have an inner balloon for deploying the antenna. The systems, devices and methods disclosed are useful for treating Barrett's Esophagus, Esophageal Adenocarcinoma, and Squamous Cell Carcinoma.