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Atrial fibrillation (AF) following cardiac surgery is an important factor contributing to postoperative morbidity. Transvenous, intracardial cardioversion (TIC) has been shown to be effective in the treatment of chronic AF, but is an invasive and cost-intensive procedure. However, TIC would definitely be a beneficial approach if recurrence of AF following TIC is low and pharmacological treatment could be avoided. Thus, we hypothesised that TIC would be superior to conventional treatment with amiodarone with respect to the conversion rate and recurrence of AF. We compared TIC and conventional amiodarone therapy in a prospective, randomised and controlled trial in patients who developed AF following cardiac surgery. Twenty-three patients developed AF out of a total of 76 patients who gave written informed consent. Eighteen of these AF patients could be randomised into two equally sized groups to receive either an ALERT TM pulmonary artery catheter and TIC, or a standard pulmonary artery catheter and treatment with amiodarone. Haemodynamic parameters were registered before intervention to exclude pulmonary hypertension or fluid overload. Rates of cardioversion were compared by a Likelyhood ratio test. Out of the nine ALERT patients, AF in five cases converted to sinus rhythm (SR) with a median of two shocks (6 J). After 24 hours however, only two patients remained in sinus rhythm. On the other hand, six of the nine patients treated with amiodarone were still in SR after 24 hours. Whereas no difference was detectable in the conversion rate, persistence of SR following TIC was low. Thus, TIC without antiarrhythmic treatment is not recommendable for the treatment of postoperative AF.