As part of a prospective study into the diagnostic role of transoesophageal echocardiography in children with complex congenital heart disease, the atrial morphology was assessed in 62 children. Using the direct visualization of atrial appendage morphology, 58 were shown to have usual atrial arrangement, two were documented to have isomerism of the right and two isomerism of the left appendages. Of those with usual arrangement, four children were demonstrated to have left juxtaposition of the atrial appendages. Only two of these patients were identified during praecordial echocardiographic re-evaluation, and three on angiocardiographic examination. Surgical confirmation was obtained in three, and juxtaposition was excluded in the remaining cases. The transoesophageal cross-sectional imaging features of left juxtaposition of the atrial appendages are unique and readily diagnostic of this entity. They include, first, a lateral deviation of the acid-portion of the atrial septum and, second, a frontal orientation of the antero-superior portion forming the floor and the posterior wall of the junction of the right-sided atrial appendage with the venous component of the atrial cavity. The knowledge of these morphologic characteristics is important, as, otherwise, this malformation may be misinterpreted as representing an atrial septal defect. The results suggest that transoesophageal echocardiography will be the most sensitive preoperative diagnostic technique in detecting or excluding juxtaposed atrial appendages.