Objective: To assess feasibility of automated edge detection in magnetic resonance (MR) flow calculations in a clinical setting with critically ill patients. Material and methods: Velocity encoded cine-MR (VEC-MR) flow measurements cross-sectional area (CSA), mean spatial velocity (MSV), instantaneous flow (IF), flow (F), 0.5 T Philips, TR 800–800, TE=8 ms, 30° flip angle, FOV 280 mm, 128×256 matrix, temporal resolution 16 time frames/RR, VENC=120 cm/s) were obtained in 20 major thoracic human vessels (ascending aorta, main, right and left pulmonary artery—AAO, MPA, RPA, LPA) of five patients, suffering from severe chronic thromboembolic pulmonary hypertension (CTEPH). Flow maps were evaluated by two independent observers using conventional manual edge detection (INTER m/m). Flow calculations were performed by one observer using both, manual and automated edge detection (INTRA m/a), by a second observer using automated edge detection two times (INTRA a/a) and by two independent observers using automated edge detection (INTER a/a). Evaluation time was measured. Linear regression analysis and Student's t-test were performed. Results: Overall regression coefficients ( r 2) for INTER m/m, INTRA m/a, INTER a/a and INTRA a/a, respectively, were as follows: CSA, 0.91, 0.91, 0.96, 0.98; MSV, 0.97, 0.99, 0.99, 0.99; IF, 0.98, 0.99, 0.99, 0.99; F, 0.98, 0.99, 0.99, 0.99. Manual CSA values differed significantly from automated data in MPA ( P=0.01), RPA ( P=0.0008) and LPA ( P=0.02). No difference was found for the other assessed parameters of the pulmonary circulation. Average evaluation time per vessel was 20.2±2.6 min for manual and 2.1±0.7 min for automated edge detection ( P<0.00001). Conclusion: The software program used provided reproducible data, lead to a 90% reduction in evaluation and calculation time and, therefore, might excel the utilization of VEC-MR flow measurements. Despite variations in the evaluation of the pulmonary circulation CSAs, flow assessment is feasible in critically ill patients.