The aim of this study was to compare the results of magnetic resonance based shunt volume measurements with the results of the invasive method by the principle of Fick. In 14 children (median age: 16.5 months) with ventricular septal defects the shunt volume was quantified by magnetic resonance flow measurements under spontaneous breathing conditions as well as with invasive angiography during one sedation. A good correlation between both methods was observed (r(2) = 0.8, p <0.0001, CI(95%) = 0.62-1.22). A tendency towards higher values in the noninvasive technique was found in the Bland-Altman plot (bias = 3.79). Magnetic resonance based shunt measurements are a reliable alternative to the invasive shunt measurement by cardiac catheterization.