OBJECTIVE--To compare the safety and efficacy of transoesophageal atrial pacing (TAP) with an easily swallowed pill electrode and direct current cardioversion (DCC) in patients with atrial flutter that was refractory to appropriate medical treatment. DESIGN--Prospective, randomised clinical trial. SETTING--Community based United States naval hospital. SUBJECTS--Twenty one consecutive patients with refractory atrial flutter selected consecutively from the inpatient cardiology consultation service. All patients were haemodynamically stable and medical treatment with a class IA or IC antiarrhythmic agent had failed. Eleven patients were treated with TAP and 10 patients were treated with DCC. INTERVENTIONS--Digoxin was given to all patients to control the ventricular rate to < 100/minute. MAIN OUTCOME MEASURE--Conversion to normal sinus rhythm and arrhythmias after cardioversion. RESULTS--Conversion to normal sinus rhythm was similar in both groups (TAP 8/11, DCC 9/10, p = 0.31). Arrhythmias after cardioversion including third degree heart block and non-sustained ventricular tachycardia were more frequent in the DCC group (TAP 0/11, DCC 6/10, p = 0.02). CONCLUSION--Transoesophageal atrial pacing with an easily swallowed pill electrode is safe, well tolerated, and is as efficacious as DCC for refractory atrial flutter.