We analyzed the natriuretic peptide type B (BNP) and A (ANP) levels in the plasma of 38 children with stable functionally univentricular heart defects, 10 of whom had undergone the first palliative step (Shunt), 13 of whom had undergone the second palliative step (Glenn), and 15 of whom had completed total cavopulmonary connection (TCPC). The levels of BNP and ANP were significantly higher after the first palliative step, 31.6 ng/l (8.3-122) (median and range) and 101.2 ng/l (17.1-203), respectively, than after the Glenn procedure, 6.7 ng/l (0.0-16.0) and 23.6 ng/l (15.7-54.4), respectively, as well as after completed TCPC, 9.0 ng/l (0.0-39.1) and 20.9 ng/l (11.2-28.3), respectively, and, in a control group of children without heart defects, 5.8 ng/l (0.0-38.7) and 32.9 ng/l (11.7-212.1), respectively (p = 0.0003 and p = 0.0003, respectively). After the first palliative step, the BNP and ANP levels were the same in children with right and left ventricular morphology (p = 0.67 and p = 0.52, respectively). After unloading the ventricle (Glenn and TCPC together), BNP levels were higher in children with right ventricular morphology compared with those with left ventricular morphology and controls (p = 0.02). Children with functionally univentricular hearts in stable condition have increased BNP and ANP levels after the first palliative procedure. After the second and third palliative steps, the BNP and ANP levels were low and similar to those of children without heart defects. However, BNP levels in children with a systemic ventricle of right ventricular morphology were higher than those in children with left ventricular morphology.