Intravenous injections of agitated saline (contrast) are used to identify right-to-left atrial shunt during transesophageal echocardiography (TEE). Color flow imaging (CFI) with TEE can be used to detect left-to-right atrial shunt but its application to detect right-to-left shunt is not known. We performed CFI and contrast during TEE in 72 patients for detection of right-to-left shunt. Frame-by-frame review of CFI demonstrated discrete laminar jets of the left side of the atrial septum at the lower or upper margin of the fossa ovalis (FO) in 41 (57%) of 72; only 22 had positive contrast. Timing of shunts was late diastolic or early systolic and not related to pulmonary venous inflow. The length of the FO at end-systole was greater in those with positive CFI compared to negative CFI (13.5 ± 5 vs 11 ± 4 mm, P = 0.02). CFI was positive for right-to-left shunt in ten of 14 with atrial septal aneurysms. Contrast was positive for right-to-left shunt in 29 (40%) of 72; all but six had positive CFI. The degree of left atrial opacification was minimal in 19 and moderate to severe in ten. FO size was greater in positive versus negative contrast (14 ± 4 vs 11 ± 5 mm, P = 0.02). Contrast was positive for shunt in ten of 14 with septal aneurysms. Thus, right-to-left atrial shunt more often occurs with increased FO size and septal aneurysms. TEE with CFI is extremely sensitive for timing and localization of atrial right-to-left shunt, but the degree of right-to-left shunt is best assessed with contrast.