Cardiac malformations with impact on loading patterns have the potential to progress to irreversible loss of ventricular function during human fetal life. N-terminal pro-B-type natriuretic peptide (nt-proBNP) is a marker of cardiac dysfunction and involved in cardiac remodeling and fibrosis. We evaluated nt-proBNP levels in the circulation of human fetuses with cardiac defects. A total of 45 cases and 75 controls during the second half of gestation were recruited. Nt-proBNP concentrations were determined in venous specimens obtained by fetal blood sampling. Results were correlated to echocardiography and Doppler studies. Mean gestational age was 26.9 weeks (range 21.0-33.4 weeks). Levels of circulating nt-proBNP were elevated in fetuses with cardiac defects (mean 6,896 ng/L (range 595-42,479 ng/L) vs. 1,867 ng/L (73-3,751 ng/L), p < 0.001). In the presence of abnormal Doppler indices a further increase was detected (mean 11,287 ng/L (range 1,403-42,479 ng/L) vs. 4,659 ng/L (595-30,848 ng/L), p = 0.021). No difference was found in fetuses with co-existing growth restriction. Malformations were classified according to their hemodynamic effect. Compared to shunt defects nt-proBNP concentrations were significantly higher in left or right ventricular outflow tract obstruction with intact ventricular septum (mean 15,639 ng/L (range 2,301-42,479 ng/L) vs. 3,891 ng/L (595-13,752 ng/L), p = 0.013), and corresponded to the degree of ventricular dysfunction. In the circulation of human fetuses with cardiac defects levels of circulating nt-proBNP are elevated. Concentrations correlate with the type of myocardial wall stress. This finding supports a role for nt-proBNP as early indicator of intrauterine cardiovascular dysfunction and cardiac remodeling.