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To conduct a prospective comparison of the accuracy of whole-body MR imaging and positron emission tomography (PET) with fluorine-18 deoxyglucose (FDG) (FDG-PET) to assess the M-stage in lung cancer patients.A total of 90 consecutive lung cancer patients (mean age = 68 years) underwent whole-body MR imaging and FDG-PET as well as other standard radiological imaging procedures before and after treatment. Probabilities of metastases on whole-body MR imaging and FDG-PET were assessed by using 5-point scoring systems on a per-site basis and on a per-patient basis. Receiver operating characteristic (ROC) curve analysis was used to compare diagnostic capabilities. Sensitivity, specificity, and accuracy were also compared by using the McNemar's test on a per-site and per-patient basis.For assessment of head and neck metastases and bone metastases, accuracies of whole-body MR imaging (95.0% and 94.8%, respectively) were significantly higher than those of FDG-PET (89.1% and 88.2%, respectively; P < 0.05). For assessment of the M-stage on a per-patient basis, accuracy of whole-body MR imaging (80.0%) was also significantly higher than that of FDG-PET (73.3%; P < 0.05).Whole-body MR imaging is an accurate diagnostic technique and may be considered at least as effective as FDG-PET for assessment of the M-stage of lung cancer patients.