The Fontan procedure is often associated with elevated right-sided pressures and low cardiac output during the early postoperative period. A dog model was established to test the effect of pulmonary artery counterpulsation after atriopulmonary anastomosis. After exclusion of the right ventricle by a purse-string suture at the right AV orifice, placed during inflow occlusion, a valved conduit was inserted between the right atrial appendage and the pulmonary artery. This created a circulatory pattern comparable to a Fontan procedure. Counterpulsation was achieved by inserting a cannula into the conduit distal to the valve in eight dogs; alternatively, in four, counterpulsation could be achieved through a 10 mm side-arm graft connected to the conduit distal to the valve. Twenty-four observations were made. Without counterpulsation the circulatory status of the dog deteriorated rapidly. Counterpulsation resulted in a mean increase in cardiac output of 48% (p less than 0.0001). Right atrial pressure fell significantly with a mean drop of 4 mm Hg (p less than 0.003). This allowed for a further increase in right-sided filling pressure by transfusion, with a subsequent further increase in cardiac output. Left atrial pressure did not change significantly unless altered by transfusion. Counterpulsation instituted through the 10 mm side-arm graft gave similar results. Pulmonary vascular resistance decreased with counterpulsation (mean decrease 35%; p less than 0.002). The use of a side-arm graft connected to the conduit after a Fontan procedure affords a clinical method of circulatory support without the need for additional surgical intervention for decannulation. These data suggest that mechanical assistance of the failing right atrium after atriopulmonary anastomosis is both feasible and effective.