Transesophageal echocardiography provides a unique view of the IAS. We reviewed results of 119 transesophageal studies (1) to study the detailed anatomy of the IAS, and (2) to determine the thickness of the IAS at different times during the cardiac cycle, (3) the effect of age, and (4) the thickness of the IAS in relation to various disease states. From the transesophageal view the IAS extends from the right posteriorly toward the left and anteriorly. The more inferior aspect of the septum courses in a more direct posteroanterior direction and is more difficult to accurately visualize. The IAS is thickest peripherally and gradually narrows toward the more centrally located fossa ovalis. A region of constant thickness is frequently present between the most peripheral aspect of the IAS and the fossa ovalis. We standardized the measurement of the thickness of the septum by measuring it only at this region of constant thickness in the plane that visualized the fossa ovalis. The mean thickness at this point was 6 +/- 2 mm. The thickness correlated weakly with the age of the patient. These results agree with previously published autopsy findings. Thickness was not affected by the presence of significant disease of the atrioventricular valves, atrial fibrillation, or an atrial septal defect. However, the thickness increased to 7 +/- 2 mm with atrial contraction during sinus rhythm (p less than 0.0001). The mean thickness of the septum primum covering the fossa ovalis was 1.8 +/- 0.7 mm.(ABSTRACT TRUNCATED AT 250 WORDS)