After modified Fontan procedures with atriopulmonary anastomoses or right atrium-right ventricle conduits, some patients have progressive exercise intolerance, effusions, arrhythmias, or protein-losing enteropathy. Theoretic advantages of a lateral atrial tunnel cavopulmonary anastomosis and published clinical results suggest that conversion of other Fontan procedures to the lateral atrial tunnel may afford clinical improvement for some patients. Eight patients (8 to 25 years old) with tricuspid atresia (n =4), double-inlet left ventricle (n = 3), and double-outlet right ventricle (n=1) underwent conversion to a lateral tunnel procedure between December 1990 and November 1994. An arbitrary clinical score was assigned before the lateral tunnel procedure and at follow-up. Before conversion, patients had decreased exercise tolerance (n = 8), arrhythmias (n = 6), effusions (n = 4), and protein-losing enteropathy (n = 8). At catheterization, all had a low cardiac index (1.9 +/- 0.7 L x min(-1) x M(-2), five had elevated pulmonary vascular resistance (>3 Wood units), and three had right pulmonary venous return obstruction by compression of an enlarged right atrium. Fenestrated lateral tunnel construction was undertaken 7.3 +/- 3.6 years after atriopulmonary anastomosis, with one early death related to low cardiac output. After the lateral tunnel procedure, two patients had no clinical improvement (no change in clinical score) but five patients had either marked or partial improvement. The right pulmonary vein compression present in three patients was resolved after conversion. The mean clinical scores improved from 4.5 +/- 1 to 3.0 +/- 2 (p < 0.04). In conclusion, conversion to a lateral tunnel procedure led to clinical improvement in five of eight patients at short-term follow-up and may be particularly indicated for patients with giant right atria or pulmonary vein compression who have symptoms. Pulmonary vein compression should be looked for in patients after modified Fontan procedures and can be relieved by conversion to the lateral tunnel procedure.