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Purpose: To apply clinical 18FDG-PET/MRI, a trade-off between image quality (IQ), diagnostic accuracy, and patient compliance is required. This study aimed to develop a mediastinal-specific 18FDG-PET/MR protocol containing dedicated MRI-sequences able to produce robust, high-quality images with great patient compliance and diagnostic performance comparable to 18FDG-PET/CT. Methods: In this study, 15 healthy subjects and 10 patients with mediastinal malignancies (i.e., 8 non-small cell lung cancer, 2 oesophageal cancer) received 18FDG-PET/MR imaging immediately after 18FDG-PET/CT. PET/MR-sequences (T1-VIBE, T2-HASTE) on a Siemens Biograph mMR scanner were optimized by varying the following parameters: breath-hold (BH, in end-expiration), fat saturation (SPAIR), and electrocardiogram-triggering (ECG, in end-diastole). IQ of each sequence-variation was qualitatively scored on a 5-point scale by medical experts and quantitatively assessed by calculating signal-to-noise ratios (SNR), contrast relative to muscle-tissue (CR), standardized-uptake-values (SUVs), and tumour-to-blood ratios (TBRs). Differences in CR determined contrast between adjacent tissues and tumour visibility. Diagnostic accuracy of 18FDG-PET/MRI was compared to 18FDG-PET/CT, in reference to clinical reports and histo-/cytopathological analyses. Results: Quantitative analysis showed that T1-VIBE images acquired with ECG-triggering presented highest SNR for soft-tissues in the mediastinum (P0.9). However, qualitative IQ of both T1-VIBE and T2-HASTE deteriorated with the addition of SPAIR. Diagnostic performance of 18FDG-PET/MR was not significantly different from 18FDG-PET/CT with similar staging, SUVs, and TBRs. However, T-status was more often over-staged on 18FDG-PET/CT, while N-status was more frequently under-staged on 18FDG-PET/MR. Conclusion: ECG-triggered T1-VIBE sequences acquired during short, multiple breath-holds are recommended for mediastinal imaging using 18FDG-PET/MR protocols. With dedicated protocols, 18FDG-PET/MR imaging could be implemented in thoracic oncology and aid in diagnostic evaluation, tailored treatment decision-making, and personalized patient care.