Balloon atrial septostomy is recommended as a standard palliative procedure in neonates with congenital heart defects who are dependent on intracardiac shunting. We describe an unusual and unreported complication associated with "bedside" balloon atrial septostomy. The umbilical venous catheterization resulted in displacement of a thrombus from the ductus venosus or the hepatic vein. We recommend careful two-dimensional echocardiographic monitoring during such procedures.