The Doppler approaches, accuracy, pitfalls and quantitation of atrial and ventricular shunts are reviewed. For both levels of shunting, Doppler demonstration of flow through the septum confirms the diagnosis and directional flow information may provide physiologic information. Shunt sizes may be measured directly by Doppler, and should be reflected by chamber dimensions and volumes. The flow disturbances present in complex malformations such as Ebstein's malformation, transposition of the great arteries with ventricular septal defect, atrial shunting before and after balloon atrial septostomy, total anomalous pulmonary venous return, closely related high velocity flows and coarctation are described. A sequential approach to each anomaly allows one to evaluate each, even if multiple defects are combined in a given patient.