Abnormalities of the mitral valve (MV) or the tricuspid valve (TV) morphology and/or function in patients with functional single ventricle may result in early morbidity and death. The purpose of this study was to determine the incidence of contralateral atrioventricular valve (AVV) pathologies in mitral valve atresia (MA) and tricuspid valve atresia (TA). We retrospectively reviewed the echocardiographic data of 50 neonates with MV and 20 with TA. Appearance of the papillary muscles, chordae tendinae, and valve leaflets was assessed. AVV regurgitation was semiquantitated by color-flow Doppler and the AVV annulus diameter was measured and indexed to body surface area. MV abnormalities were found in 9 of 20 (45%) of patients with TA. The MV was myxomatous in 9 patients, the leaflets were redundant in 5 patients, and prolapsing occurred in 4 patients. Mild regurgitation was found in 2 patients. In 18 of 20 (90%) patients MV annulus size was larger than 95% of predicted normal values. TV abnormalities were found in 12 of 50 (24%) patients with MA. The TV was myxomatous in 4 patients, prolapsing in 2, and redundant in 3, and moderate TV regurgitation was found in 3 patients. In 29 of 50 (58%) patients TV annulus size was larger than 95% of predicted normal values. Contralateral AVV abnormalities in tricuspid and mitral valve atresia are common and should be assessed carefully before surgical procedures.