The measurement of plasma B-type natriuretic peptide (BNP) has emerged as a useful biomarker of heart failure in patients with cardiomyopathy. The pathophysiology of heart failure in single ventricle (SV) circulation may be distinct from that of cardiomyopathies. A distinct pattern of BNP elevation in heart failure in the SV population was hypothesized: it is elevated in heart failure secondary to ventricular dysfunction but not in isolated cavopulmonary failure. BNP was measured prospectively in SV patients at catheterization (n = 22) and when assessing for heart failure (n = 11) (7 normal controls). Of 33 SV subjects (median age 62 months), 13 had aortopulmonary connections and 20 had cavopulmonary connections. Median and mean +/- SD BNP levels by shunt type were 184 and 754 +/- 1,086 pg/ml in the patients with aortopulmonary connections, 38 and 169 +/- 251 pg/ml in the patients with cavopulmonary connections, and 10 and 11 +/- 5 pg/ml in normal controls, respectively (p = 0.004). Median systemic ventricular end-diastolic pressure (8mm Hg, R = 0.45), mean pulmonary artery pressure (14.5 mm Hg, R = 0.62), and mean right atrial pressure (6.5 mm Hg, R = 0.54) were correlated with plasma BNP. SV subjects with symptomatic heart failure from dysfunctional systemic ventricles had median and mean +/- SD BNP levels of 378 and 714 +/- 912 pg/ml (n = 18) compared with patients with isolated failed Glenn or Fontan connections (19 and 23 +/- 16 pg/ml [n = 7, p = 0.001]) and those with no heart failure (22 and 22 +/- 12 pg/ml [n = 8, p = 0.001]). Excluding the group with cavopulmonary failure, the severity of heart failure from systemic ventricular dysfunction was associated with plasma BNP. In conclusion, plasma BNP is elevated in SV patients with systemic ventricular or left-sided cardiac failure. BNP is not elevated in patients missing a pulmonary ventricle with isolated cavopulmonary failure.