OBJECTIVE To compare the diagnostic accuracy of whole-body PET/CT and integrated PET/MR in relation to the total scan time durations. METHODS One hundred and twenty-three (123) patients (40 males and 83 females; mean age 59.6 years; range 20-83 years) with confirmed primary cancer and clinical suspicion of metastatic disease underwent whole-body 18F-FDG-PET/CT and 18F-FDG-PET/MR. Data acquisition was done after intravenous administration of 110-301 MBq radioactivity of 18F-FDG, and PET/MR data were acquired after the PET/CT data acquisition. The mean uptake times for PET/CT and PET/MR acquisition were 68.0 ± 8.0 and 98.0 ± 14 min, respectively. Total scan time was 20.0 and 25.0 min for whole-body PET/CT and PET/MR imaging. RESULTS The reconstructed PET/CT and PET/MR data detected 333/355 (93.8 %) common lesions in 111/123 (90.2 %) patients. PET/CT and PET/MR alone detected 348/355 and 340/355 lesions, respectively. No significant (p = 0.08) difference was observed for the overall detection efficiency between the two techniques. On the other hand, a significant difference was observed between the two techniques for the detection of lung (p = 0.003) and cerebrospinal (p = 0.007) lesions. The 15 lesions identified by PET/CT only included 8 lung, 3 lymph nodes, 2 bone, and 1 each of peritoneal and adrenal gland lesions. On the other hand, 7 (6 brain metastatic lesions and 1 bone lesion) were identified by PET/MR only. CONCLUSIONS Integrated PET/MR is a feasible whole-body imaging modality and may score better than PET/CT for the detection of brain metastases. To further prove diagnostic utility, this technique requires further clinical validation.