Segmentation of the lungs within magnetic resonance (MR) scans is a necessary step in the computer-based analysis of thoracic MR images. This process is often confounded by image acquisition artifacts and disease-induced morphological deformation. We have developed an automated method for lung segmentation that is insensitive to these complications. The automated method was applied to 23 thoracic MR scans (413 sections) obtained from 10 patients. Two radiologists manually outlined the lung regions in a random sample of 101 sections (n=202 lungs), and the extent to which disease or artifact confounded lung border visualization was evaluated. Accuracy of lung regions extracted by the automated segmentation method was quantified by comparison with the radiologist-defined lung regions using an area overlap measure (AOM) that ranged from 0 (disjoint lung regions) to 1 (complete overlap). The AOM between each observer and the automated method was 0.82 when averaged over all lungs. The average AOM in the lung bases, where lung segmentation is most difficult, was 0.73.