Objective-To examine, using transoesophageal echocardiography, the possible disturbances of left atrial appendage function during VVI and DDD pacing in patients with a normal atrium paced with a dual chamber system. Design-Randomised controlled trial. Setting-Tertiary care centre. Patients-22 patients (mean age 68 (SD 6) years) who had been paced with dual chamber pacemakers for at least six months. Exclusion criteria were valvar disease, cardiomyopathy, hypertension, and diabetes mellitus. Interventions-All patients underwent a transoesophageal echocardiographic evaluation of left atrial appendage function under DDD and WI modes in random order. Measurements were made after at least two months' pacing in each mode. Main outcome measures-Echocardiographic indices of left atrial appendage flow under both pacing modes. Results-All 22 patients had higher emptying and filling flow velocities under DDD than under WI mode. The filling and emptying flow velocity integrals were also significantly higher under DDD mode (P < 0.001, P = 0.019). Conclusions-Left atrial appendage function, as reflected in indices of emptying and filling assessed by transoesophageal echocardiography, is significantly different with DDD than with WI pacing. This may explain the higher incidence of thromboembolic episodes in patients paced under WI mode.