The objective of this study was to asses the feasibility and accuracy of magnetic resonance (MR) velocity mapping to calculate pulmonary-to-systemic flow ratio (Qp:Qs) in patients with a suspected or diagnosed atrial-level shunt. During a one-year period, all patients referred to our department for further evaluation of an atrial-level shunt underwent the same imaging protocol. Multiphase-multisection gradient-echo MR image sets of the heart were acquired to measure left and right ventricular stroke volumes for validation. Ascending aorta and main pulmonary artery volume flow were measured with MR velocity mapping. Qp:Qs ratios were calculated from both stroke volume data and flow data. Twelve patients, including 6 children, were studied. Six patients had an established diagnosis of atrial septal defect, and the other 6 patients were suspected to have an atrial-level shunt. Measurements of left and right ventricular stroke corresponded closely with those of aortic (r = 0.98) and pulmonary flow (r = 0.99) respectively, and Qp:Qs flow ratios agreed with stroke volume ratios (r = 0.92). In 5 patients with a suspected shunt, the diagnosis could be rejected. Shunts were demonstrated in the other 7 patients. M(r) velocity mapping offers an accurate method to measure aortic and pulmonary artery volume flow that can be useful in the evaluation of atrial-level shunts, in order to establish a definite diagnosis and/or to quantify the Qp:Qs ratio.